Quantification of the hydrophobic interaction by simulations of the aggregation of small hydrophobic solutes in water

PubMed Central

Raschke, Tanya M.; Tsai, Jerry; Levitt, Michael

2001-01-01

The hydrophobic interaction, the tendency for nonpolar molecules to aggregate in solution, is a major driving force in biology. In a direct approach to the physical basis of the hydrophobic effect, nanosecond molecular dynamics simulations were performed on increasing numbers of hydrocarbon solute molecules in water-filled boxes of different sizes. The intermittent formation of solute clusters gives a free energy that is proportional to the loss in exposed molecular surface area with a constant of proportionality of 45 ± 6 cal/mol⋅Å2. The molecular surface area is the envelope of the solute cluster that is impenetrable by solvent and is somewhat smaller than the more traditional solvent-accessible surface area, which is the area transcribed by the radius of a solvent molecule rolled over the surface of the cluster. When we apply a factor relating molecular surface area to solvent-accessible surface area, we obtain 24 cal/mol⋅Å2. Ours is the first direct calculation, to our knowledge, of the hydrophobic interaction from molecular dynamics simulations; the excellent qualitative and quantitative agreement with experiment proves that simple van der Waals interactions and atomic point-charge electrostatics account for the most important driving force in biology. PMID:11353861

Theoretical study of the electronic and optical properties of photochromic dithienylethene derivatives connected to small gold clusters.

PubMed

Perrier, Aurélie; Maurel, François; Aubard, Jean

2007-10-04

In the course of developing electronic devices on a molecular scale, dithienylethenes photochromic molecules constitute promising candidates for optoelectronic applications such as memories and switches. There is thus a great interest to understand and control the switching behavior of photochromic compounds deposited on metallic surfaces or nanoparticles. Within the framework of the density functional theory, we studied the effect of small gold clusters (Au3 and Au9) on the electronic structure and absorption spectrum of a model dithienylethene molecule. The molecular orbital interactions between the photochromic molecule and the gold cluster made it possible to rationalize some experimental findings (Dulic, D.; van der Molen, S. J.; Kudernac, T.; Jonkman, H. T.; de Jong, J. J. D.; Bowden, T. N.; van Esch, J.; Feringa, B. L.; van Wees, B. J. Phys. Rev. Lett. 2003, 91, 207402). For the closed-ring isomer, grafting a photochromic molecule on a small gold cluster does not change the characteristics of the electronic transition involved in the ring-opening reaction. On the opposite, the absorption spectrum of the photochromic open-ring isomer is strongly modified by the inclusion of the metallic cluster. In agreement with experimental results, our study thus showed that the cycloreversion reaction which involves the closed-ring isomer should be still possible, whereas the ring-closure reaction which involves the open-ring isomer should be inhibited. Connecting a dithienylethene molecule to a small gold cluster hence provides a qualitative comprehension of the photochromic activities of dithienylethenes connected to a gold surface.

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

PubMed

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.

Organomimetic clusters: Precision in 3D

NASA Astrophysics Data System (ADS)

Majewski, Marek B.; Howarth, Ashlee J.; Farha, Omar K.

2017-04-01

Biomimetic molecules that can be easily tailored offer numerous opportunities. Now, boron-based clusters have been shown to be excellent biomimetics. The ease with which the cluster surfaces can be modified stands to change how chemists might go about preparing materials for imaging, drug delivery and other applications.

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

NASA Astrophysics Data System (ADS)

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.

Significant Transient Mobility of Platinum Clusters via a Hot Precursor State on the Alumina Surface.

PubMed

Beniya, Atsushi; Hirata, Hirohito; Watanabe, Yoshihide

2016-11-17

Relaxation dynamics of hot metal clusters on oxide surfaces play a crucial role in a variety of physical and chemical processes. However, their transient mobility has not been investigated as much as other systems such as atoms and molecules on metal surfaces due to experimental difficulties. To study the role of the transient mobility of clusters on the oxide surface, we investigated the initial adsorption process of size-selected Pt clusters on a thin Al 2 O 3 film. Soft-landing the size-selected clusters while suppressing the thermal migration resulted in the transient migration controlling the initial adsorption states as an isolated and aggregated cluster, as revealed using scanning tunneling microscopy. We demonstrate that transient migration significantly contributes to the initial cluster adsorption process; the cross section for aggregation is seven times larger than the expected value from geometrical considerations, indicating that metal clusters are highly mobile during a energy dissipation process on the oxide surface.

Metal nanostructures: from clusters to nanocatalysis and sensors

NASA Astrophysics Data System (ADS)

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.

Analyzing multistep homogeneous nucleation in vapor-to-solid transitions using molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Tanaka, Kyoko K.; Diemand, Jürg; Tanaka, Hidekazu; Angélil, Raymond

2017-08-01

In this paper, we present multistep homogeneous nucleations in vapor-to-solid transitions as revealed by molecular dynamics simulations on Lennard-Jones molecules, where liquidlike clusters are created and crystallized. During a long, direct N V E (constant volume, energy, and number of molecules) involving the integration of (1.9 -15 )× 106 molecules in up to 200 million steps (=4.3 μ s ), crystallization in many large, supercooled nanoclusters is observed once the liquid clusters grow to a certain size (˜800 molecules for the case of T ≃0.5 ɛ /k ). In the simulations, we discovered an interesting process associated with crystallization: the solid clusters lost 2-5 % of their mass during crystallization at low temperatures below their melting temperatures. Although the crystallized clusters were heated by latent heat, they were stabilized by cooling due to evaporation. The clusters crystallized quickly and completely except at surface layers. However, they did not have stable crystal structures, rather they had metastable structures such as icosahedral, decahedral, face-centered-cubic-rich (fcc-rich), and hexagonal-close-packed-rich (hcp-rich). Several kinds of cluster structures coexisted in the same size range of ˜1000 -5000 molecules. Our results imply that multistep nucleation is a common first stage of condensation from vapor to solid.

A DFT study on surface-enhanced Raman spectroscopy of aromatic dithiol derivatives adsorbed on gold nanojunctions

NASA Astrophysics Data System (ADS)

You, Tingting; Lang, Xiufeng; Huang, Anping; Yin, Penggang

2018-01-01

A computational study on aromatic dithiol derivatives (HS-Ar-X-Ar-SH, X = O, S, Se, NH, CH2, Ndbnd N, CHdbnd CH, Ctbnd C) interacting with gold cluster(s) was presented to investigate the chemical enhancement mechanism related to surface-enhanced Raman spectroscopy (SERS) for molecular junctions. Density functional theory (DFT) were performed on derivatives molecules as well as their single-end-linked (SEL) or double-end-linked (DEL) complexes for geometric, spectra, electronic and excitation properties, leading to discussions on dominant factor during SERS process. The resulted enhancement factors of SEL and DEL complexes exhibited specific dependency on linking atom or functional group between two phenyls, which was in accordance with the variation of polarizabilities and molecule-cluster transition energy.

Photodissociation and caging of HBr and HI molecules on the surface of large rare gas clusters.

PubMed

Baumfalk, R; Nahler, N H; Buck, U

2001-01-01

Photodissociation experiments were carried out at a wavelength of 243 nm for single HBr and HI molecules adsorbed on the surface of large Nen, Arn, Krn and Xen clusters. The average size is about = 130; the size ranges = 62-139 for the system HBr-Arn and = 110-830 for HI-Xen were covered. In this way the dependence of the photodissociation dynamics on both the size and the rare gas host cluster was investigated. The main observable is the kinetic energy distribution of the outgoing H atoms. The key results are that we do not find any size dependence for either system but that we observe a strong dependence on the rare gas clusters. All systems exhibit H atoms with no energy loss that indicate direct cage exit and those with nearly zero energy that are an indication of complete caging. The intensity ratio of caged to uncaged H atoms is largest for Nen, decreases with increasing mass of the cage atoms, and is weakest for Xen. On the basis of accompanying calculations this behaviour is attributed to the large amplitude motion of the light H atom. This leads to direct cage exit and penetration of the atom through the cluster with different energy transfer per collision depending on the rare gas atoms. The differences between HBr and HI molecules are attributed to different surface states, a flat and an encapsulated site.

Isolated single-molecule magnets on native gold.

PubMed

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.

Modeling solute clustering in the diffusion layer around a growing crystal.

PubMed

Shiau, Lie-Ding; Lu, Yung-Fang

2009-03-07

The mechanism of crystal growth from solution is often thought to consist of a mass transfer diffusion step followed by a surface reaction step. Solute molecules might form clusters in the diffusion step before incorporating into the crystal lattice. A model is proposed in this work to simulate the evolution of the cluster size distribution due to the simultaneous aggregation and breakage of solute molecules in the diffusion layer around a growing crystal in the stirred solution. The crystallization of KAl(SO(4))(2)12H(2)O from aqueous solution is studied to illustrate the effect of supersaturation and diffusion layer thickness on the number-average degree of clustering and the size distribution of solute clusters in the diffusion layer.

[Achene morphology cluster analysis of Taraxacum F. H. Wigg. from northeast China and molecule systematics evidence determined by SRAP].

PubMed

Li, Hai-juan; Zhao, Xin; Jia, Qing-fei; Li, Tian-lai; Ning, Wei

2012-08-01

The achenes morphological and micro-morphological characteristics of six species of genus Taraxacum from northeastern China as well as SRAP cluster analysis were observed for their classification evidences. The achenes were observed by microscope and EPMA. Cluster analysis was given on the basis of the size, shape, cone proportion, color and surface sculpture of achenes. The Taraxacum inter-species achene shape characteristic difference is obvious, particularly spinulose distribution and size, achene color and achene size; with the Taraxacum plant achene shape the cluster method T. antungense Kitag. and the T. urbanum Kitag. should combine for the identical kind; the achene morphology cluster analysis and the SRAP tagged molecule systematics's cluster result retrieves in the table with "the Chinese flora". The class group to divide the result is consistent. Taraxacum plant achene shape characteristic stable conservative, may carry on the inter-species division and the sibship analysis according to the achene shape characteristic combination difference; the achene morphology cluster analysis as well as the SRAP tagged molecule systematics confirmation support dandelion classification result of "the Chinese flora".

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

PubMed

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.

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

NASA Technical Reports Server (NTRS)

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.

Hydration of Atmospheric Molecular Clusters: Systematic Configurational Sampling.

PubMed

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.

Manipulation of Origin of Life Molecules: Recognizing Single-Molecule Conformations in β-Carotene and Chlorophyll-a/β-Carotene Clusters

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

Ngo, Anh T.; Skeini, Timur; Iancu, Violeta

Carotenoids and chlorophyll are essential parts of plant leaves and are involved in photosynthesis, a vital biological process responsible for the origin of life on Earth. Here, we investigate how beta-carotene and chlorophyll-a form mixed molecular phases On a Au(111) surface using low-temperature scanning tunneling microscopy and molecular manipulation at the single-molecule level supported by density functional theory calculations. By isolating individual molecules from nanoscale molecular clusters with a scanning tunneling microscope tip, we are able to identify five beta-carotene conformations including a structure exhibiting a three-dimensional conformation. Furthermore, molecular resolution images enable direct visualization of beta-carotene/chlorophyll-a clsuters, with intimatemore » structural details highlighting how they pair: beta-carotene preferentially positions next to chlorophyll-a and induces switching of chlorophyll-a from straight to several bent tail conformations in the molecular clusters.« less

Deprotonated Water Dimers: The Building Blocks of Segmented Water Chains on Rutile RuO2(110)

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

Mu, Rentao; Cantu Cantu, David; Glezakou, Vassiliki Alexandra

2015-10-15

Despite the importance of RuO2 in photocatalytic water splitting and catalysis in general, the interactions of water with even its most stable (110) surface are not well-understood. In this study we employ a combination of high-resolution scanning tunneling microscopy imaging with density functional theory based ab initio molecular dynamics, and we follow the formation and binding of linear water clusters on coordinatively unsaturated ruthenium rows. We find that clusters of all sizes (dimers, trimers, tetramers, extended chains) are stabilized by donating one proton per every two water molecules to the surface bridge bonded oxygen sites, in contrast with water monomersmore » that do not show a significant propensity for dissociation. The clusters with odd number of water molecules are less stable than the clusters with even number, and are generally not observed under thermal equilibrium. For all clusters with even numbers, the dissociated dimers represent the fundamental building blocks with strong intra-dimer hydrogen bonds and only very weak inter-dimer interactions resulting in segmented water chains.« less

Oriented xenon hydride molecules in the gas phase

NASA Astrophysics Data System (ADS)

Buck, Udo; Fárník, Michal

The production of the xenon hydride molecules HXeX with X = I and Cl in the gas phase is reviewed. These molecules are generated by the photolysis of the hydrogen halide HI and HCl molecules on the surface of large xenon Xen clusters. Molecular dynamics simulations show that the flexible H atoms react with the heavy XeX moiety and form the desired molecules with nearly no rotational motion. They are observed by photodissociation with subsequent detection of the kinetic energy of the H atom fragment. During the generating process, the cluster starts to evaporate and the hydride molecule is left essentially free. For further discrimination against the H atom fragments from HX, the HXeX molecules are oriented in a combined pulsed laser field and a weak electrostatic field. The three topics which represent the background of our experiments are briefly reviewed: the nature and generation of rare gas hydrides, the alignment and orientation of molecules in electric fields, and the photodissociation of selected molecules in rare gas clusters. The conditions for detecting them in the gas phase are discussed. This is the trade off between the stability, which requires high electron affinity, and the conditions for orientation, which necessitate large polarizability anisotropies and dipole moments. Finally the prospects of detecting other classes of molecules are discussed.

Site-specific vibrational spectral signatures of water molecules in the magic H3O+(H2O)20 and Cs+(H2O)20 clusters

PubMed Central

Fournier, Joseph A.; Wolke, Conrad T.; Johnson, Christopher J.; Johnson, Mark A.; Heine, Nadja; Gewinner, Sandy; Schöllkopf, Wieland; Esser, Tim K.; Fagiani, Matias R.; Knorke, Harald; Asmis, Knut R.

2014-01-01

Theoretical models of proton hydration with tens of water molecules indicate that the excess proton is embedded on the surface of clathrate-like cage structures with one or two water molecules in the interior. The evidence for these structures has been indirect, however, because the experimental spectra in the critical H-bonding region of the OH stretching vibrations have been too diffuse to provide band patterns that distinguish between candidate structures predicted theoretically. Here we exploit the slow cooling afforded by cryogenic ion trapping, along with isotopic substitution, to quench water clusters attached to the H3O+ and Cs+ ions into structures that yield well-resolved vibrational bands over the entire 215- to 3,800-cm−1 range. The magic H3O+(H2O)20 cluster yields particularly clear spectral signatures that can, with the aid of ab initio predictions, be traced to specific classes of network sites in the predicted pentagonal dodecahedron H-bonded cage with the hydronium ion residing on the surface. PMID:25489068

Site-specific vibrational spectral signatures of water molecules in the magic H 3O +(H 2O) 20 and Cs +(H 2O) 20 clusters

DOE PAGES

Fournier, Joseph A.; Wolke, Conrad T.; Johnson, Christopher J.; ...

2014-12-08

Here, theoretical models of proton hydration with tens of water molecules indicate that the excess proton is embedded on the surface of clathrate-like cage structures with one or two water molecules in the interior. The evidence for these structures has been indirect, however, because the experimental spectra in the critical H-bonding region of the OH stretching vibrations have been too diffuse to provide band patterns that distinguish between candidate structures predicted theoretically. Here we exploit the slow cooling afforded by cryogenic ion trapping, along with isotopic substitution, to quench water clusters attached to the H 3O + and Cs +more » ions into structures that yield well-resolved vibrational bands over the entire 215- to 3,800-cm -1 range. The magic H 3O +(H 2O) 20 cluster yields particularly clear spectral signatures that can, with the aid of ab initio predictions, be traced to specific classes of network sites in the predicted pentagonal dodecahedron H-bonded cage with the hydronium ion residing on the surface.« less

Experimental and theoretical study of the pyrrole cluster photochemistry: Closing the {pi}{sigma}{sup *} dissociation pathway by complexation

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

Poterya, Viktoriya; Profant, Vaclav; Farnik, Michal

Photolysis of size selected pyrrole clusters has been investigated and compared to the photolysis of an isolated pyrrole molecule. Experimentally, size distributions of different mean cluster sizes (n=3 and n>>5) have been prepared in supersonic expansions and the clusters were photolyzed at 243 and 193 nm. The kinetic energy distributions of the H photofragments have been measured. The distributions exhibit a bimodal character with fast and slow H-fragment peaks similar to the spectra of the bare molecule. However, with increasing cluster size the slow component gains intensity with respect to the fast one. A similar effect is observed with increasingmore » the excitation energy from 243 to 193 nm. Theoretical calculations at the CASSCF/CASPT2 level have been performed for bare and complexed pyrroles (pyrrole is complexed with an argon atom and with another pyrrole unit). Combination of theoretical and experimental approaches leads to the conclusion that the direct dissociative pathway along the {pi}{sigma}{sup *} potential energy surface in the N-H stretch coordinate is closed by the presence of the solvent molecule. This pathway is an important channel leading to the fast H atoms in the dissociation of the bare molecule. The solvent molecule influences significantly the electronic structure in the Rydberg-type {pi}{sigma}{sup *} state while it has little influence on the valence states. The slow channel is mostly populated by the out-of-plane deformation mode which is also not influenced by solvation. We have also studied other possible reaction channels in pyrrole clusters (hydrogen transfer, dimerization). The present study shows that more insight into the bulk behavior of biologically relevant molecules can be gained from cluster studies.« less

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

PubMed

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.

Formation of novel rare-gas-containing molecules by molecular photodissociation in clusters.

PubMed

Cohen, A; Niv, M Y; Gerber, R B

2001-01-01

Recent work by Räsänen and coworkers showed that photolysis of hydrides in rare-gas matrices results in part in formation of novel, rare-gas-containing molecules. Thus, photolysis of HCl in Xe and of H2O in Xe result respectively in formation of HXeCl and HXeOH in the Xe matrices. Ab initio calculations show that the compounds HRgY so formed are stable in isolation, and that by the strength and nature of the bonding these are molecules, very different from the corresponding weakly bound clusters Rg...HY. This paper presents a study of the formation mechanism of HRgY following the photolysis of HY in clusters Rgn(HY). Calculations are described for HXeCl, as a representative example. Potential energy surfaces that govern the formation of HXeCl in the photolysis of HCl in xenon clusters are obtained, and the dynamics on these surfaces is analyzed, partly with insight from trajectories of molecular dynamics simulations. The potential surfaces are obtained by a new variant of the DIM (diatomics in molecules) and DIIS (diatomics in ionic systems) models. Non-adiabatic couplings are also obtained. The main results are: (1) Properties of HXeCl predicted by the DIM-DIIS model are in reasonable accord with results of ab initio calculations. (2) The potential along the isomerization path HXeCl-->Xe...HCl predicted by DIM is in semiquantitative accord with the ab initio results. (3) Surface-hopping molecular dynamics simulations of the process in clusters, with "on the fly" calculations of the DIM-DIIS potentials and non-adiabatic couplings are computationally feasible. (4) Formation of HXeCl, following photolysis of HCl in Xe54(HCl), requires cage-exit of the H atom as a precondition. The H atom and the Cl can then attack the same Xe atom on opposite sides, leading to charge transfer and production of the ionic HXeCl. (5) Non-adiabatic processes play an important role, both in the reagent configurations, and at the charge-transfer stage. The results open the way to predictions of the formation of new HRgY species.

Modeling the self-assembly of functionalized fullerenes on solid surfaces using Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Bubnis, Gregory J.

Since their discovery 25 years ago, carbon fullerenes have been widely studied for their unique physicochemical properties and for applications including organic electronics and photovoltaics. For these applications it is highly desirable for crystalline fullerene thin films to spontaneously self-assemble on surfaces. Accordingly, many studies have functionalized fullerenes with the aim of tailoring their intermolecular interactions and controlling interactions with the solid substrate. The success of these rational design approaches hinges on the subtle interplay of intermolecular forces and molecule-substrate interactions. Molecular modeling is well-suited to studying these interactions by directly simulating self-assembly. In this work, we consider three different fullerene functionalization approaches and for each approach we carry out Monte Carlo simulations of the self-assembly process. In all cases, we use a "coarse-grained" molecular representation that preserves the dominant physical interactions between molecules and maximizes computational efficiency. The first approach we consider is the traditional gold-thiolate SAM (self-assembled monolayer) strategy which tethers molecules to a gold substrate via covalent sulfur-gold bonds. For this we study an asymmetric fullerene thiolate bridged by a phenyl group. Clusters of 40 molecules are simulated on the Au(111) substrate at different temperatures and surface coverage densities. Fullerenes and S atoms are found to compete for Au(111) surface sites, and this competition prevents self-assembly of highly ordered monolayers. Next, we investigate self-assembled monolayers formed by fullerenes with hydrogen-bonding carboxylic acid substituents. We consider five molecules with different dimensions and symmetries. Monte Carlo cooling simulations are used to find the most stable solid structures of clusters adsorbed to Au(111). The results show cases where fullerene-Au(111) attraction, fullerene close-packing, and hydrogen-bonding interactions can cooperate to guide self-assembly or compete to hinder it. Finally, we consider three bis-fullerene molecules, each with a different "bridging group" covalently joining two fullerenes. To effectively study the competing "standing-up" and "lying-down" morphologies, we use Monte Carlo simulations in conjunction with replica exchange and force field biasing methods. For clusters adsorbed to smooth model surfaces, we determine free energy landscapes and demonstrate their utility for rationalizing and predicting self-assembly.

DFT STUDY OF CO AND NO ADSORPTION ON BORON NITRIDE (BN)n = 3 - 5 NANOCLUSTERS

NASA Astrophysics Data System (ADS)

Zahedi, Ehsan; Pangh, Abdolhakim; Ghorbanpour, Hamed

2015-11-01

Interaction of CO and NO molecules by different orientations on (BN)n=3-5 clusters have been studied at the B3LYP/6-311+G* level of theory. Total electronic energies have been corrected for geometrical counterpoise (gCP) and dispersion (D3) energies at the B3LYP/6-31G* level. Formation of a new sigma bond between the gas and (BN)3 cluster, atom in molecules (AIM) results, density of states spectrums (DOS), molecular electrostatic potential (MEP) surfaces, and visualization of wave function of molecular orbitals in the nearest bonding regions to the Fermi level have confirmed that adsorption of CO by carbon end atom, and NO by nitrogen end atom is covalent in nature, so that the charge transfer is occurred from gas molecule to the cluster.

Sequential water molecule binding enthalpies for aqueous nanodrops containing a mono-, di- or trivalent ion and between 20 and 500 water molecules† †Electronic supplementary information (ESI) available: Detailed description of the experimental and computational modeling methods. Isolation, BIRD and UVPD sequence for [Ru(NH3)6]3+·(H2O)169–171, nanoESI spectra for 2+ and 3+ ions. Detailed description of the isotope distribution simulation program. Comparison between experimental and simulated 1+, 2+ and 3+ ion isotope distributions. Wavelength dependence of the deduced sequential binding enthalpies. Comparison of experimental UVPD binding enthalpies to the liquid drop model at different temperatures. Complete list of binding enthalpies and average number of water molecules lost upon UVPD. See DOI: 10.1039/c6sc04957e Click here for additional data file.

PubMed Central

Heiles, Sven; Cooper, Richard J.; DiTucci, Matthew J.

2017-01-01

Sequential water molecule binding enthalpies, ΔH n,n–1, are important for a detailed understanding of competitive interactions between ions, water and solute molecules, and how these interactions affect physical properties of ion-containing nanodrops that are important in aerosol chemistry. Water molecule binding enthalpies have been measured for small clusters of many different ions, but these values for ion-containing nanodrops containing more than 20 water molecules are scarce. Here, ΔH n,n–1 values are deduced from high-precision ultraviolet photodissociation (UVPD) measurements as a function of ion identity, charge state and cluster size between 20–500 water molecules and for ions with +1, +2 and +3 charges. The ΔH n,n–1 values are obtained from the number of water molecules lost upon photoexcitation at a known wavelength, and modeling of the release of energy into the translational, rotational and vibrational motions of the products. The ΔH n,n–1 values range from 36.82 to 50.21 kJ mol–1. For clusters containing more than ∼250 water molecules, the binding enthalpies are between the bulk heat of vaporization (44.8 kJ mol–1) and the sublimation enthalpy of bulk ice (51.0 kJ mol–1). These values depend on ion charge state for clusters with fewer than 150 water molecules, but there is a negligible dependence at larger size. There is a minimum in the ΔH n,n–1 values that depends on the cluster size and ion charge state, which can be attributed to the competing effects of ion solvation and surface energy. The experimental ΔH n,n–1 values can be fit to the Thomson liquid drop model (TLDM) using bulk ice parameters. By optimizing the surface tension and temperature change of the logarithmic partial pressure for the TLDM, the experimental sequential water molecule binding enthalpies can be fit with an accuracy of ±3.3 kJ mol–1 over the entire range of cluster sizes. PMID:28451364

Correlation Functions Quantify Super-Resolution Images and Estimate Apparent Clustering Due to Over-Counting

PubMed Central

Veatch, Sarah L.; Machta, Benjamin B.; Shelby, Sarah A.; Chiang, Ethan N.; Holowka, David A.; Baird, Barbara A.

2012-01-01

We present an analytical method using correlation functions to quantify clustering in super-resolution fluorescence localization images and electron microscopy images of static surfaces in two dimensions. We use this method to quantify how over-counting of labeled molecules contributes to apparent self-clustering and to calculate the effective lateral resolution of an image. This treatment applies to distributions of proteins and lipids in cell membranes, where there is significant interest in using electron microscopy and super-resolution fluorescence localization techniques to probe membrane heterogeneity. When images are quantified using pair auto-correlation functions, the magnitude of apparent clustering arising from over-counting varies inversely with the surface density of labeled molecules and does not depend on the number of times an average molecule is counted. In contrast, we demonstrate that over-counting does not give rise to apparent co-clustering in double label experiments when pair cross-correlation functions are measured. We apply our analytical method to quantify the distribution of the IgE receptor (FcεRI) on the plasma membranes of chemically fixed RBL-2H3 mast cells from images acquired using stochastic optical reconstruction microscopy (STORM/dSTORM) and scanning electron microscopy (SEM). We find that apparent clustering of FcεRI-bound IgE is dominated by over-counting labels on individual complexes when IgE is directly conjugated to organic fluorophores. We verify this observation by measuring pair cross-correlation functions between two distinguishably labeled pools of IgE-FcεRI on the cell surface using both imaging methods. After correcting for over-counting, we observe weak but significant self-clustering of IgE-FcεRI in fluorescence localization measurements, and no residual self-clustering as detected with SEM. We also apply this method to quantify IgE-FcεRI redistribution after deliberate clustering by crosslinking with two distinct trivalent ligands of defined architectures, and we evaluate contributions from both over-counting of labels and redistribution of proteins. PMID:22384026

Bonding and vibrations of CO molecules adsorbed at transition metal impurity sites on the MgO (001) surface. A density functional model cluster study

NASA Astrophysics Data System (ADS)

Neyman, K. M.; Rösch, N.

1993-11-01

First principles density functional cluster investigations of adsorption at the (001) surface of pure and doped magnesium oxide are carried out to characterize and compare the interaction of CO molecules with main group (Mg 2+) and d metal (Co 2+, Ni 2+, Cu 2+) surface cationic centers of the ionic substrate. The geometry of the adsorption complexes, the binding mechanism and spectroscopic manifestations of the surface species are analyzed. Special attention is payed to vibrational frequencies and intensities. The calculations qualitatively reproduce observed trends in the adsorption-induced frequency shifts for the series of the surface aggregates Mg 5cCO→Ni 5cCO→CO 5cCO and the corresponding change of the infrared intensities of the CO vibrational mode. For the transition metal impurity sites these results are rationalized in terms of a small, but notable Md πCOπ interaction.

Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design

NASA Astrophysics Data System (ADS)

Lerner, Michael G.; Meagher, Kristin L.; Carlson, Heather A.

2008-10-01

Use of solvent mapping, based on multiple-copy minimization (MCM) techniques, is common in structure-based drug discovery. The minima of small-molecule probes define locations for complementary interactions within a binding pocket. Here, we present improved methods for MCM. In particular, a Jarvis-Patrick (JP) method is outlined for grouping the final locations of minimized probes into physical clusters. This algorithm has been tested through a study of protein-protein interfaces, showing the process to be robust, deterministic, and fast in the mapping of protein "hot spots." Improvements in the initial placement of probe molecules are also described. A final application to HIV-1 protease shows how our automated technique can be used to partition data too complicated to analyze by hand. These new automated methods may be easily and quickly extended to other protein systems, and our clustering methodology may be readily incorporated into other clustering packages.

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

NASA Technical Reports Server (NTRS)

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.

Conserved water molecules in bacterial serine hydroxymethyltransferases.

PubMed

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.

Recent developments in the kinetic theory of nucleation.

PubMed

Ruckenstein, E; Djikaev, Y S

2005-12-30

A review of recent progress in the kinetics of nucleation is presented. In the conventional approach to the kinetic theory of nucleation, it is necessary to know the free energy of formation of a new-phase particle as a function of its independent variables at least for near-critical particles. Thus the conventional kinetic theory of nucleation is based on the thermodynamics of the process. The thermodynamics of nucleation can be examined by using various approaches, such as the capillarity approximation, density functional theory, and molecular simulation, each of which has its own advantages and drawbacks. Relatively recently a new approach to the kinetics of nucleation was proposed [Ruckenstein E, Nowakowski B. J Colloid Interface Sci 1990;137:583; Nowakowski B, Ruckenstein E. J Chem Phys 1991;94:8487], which is based on molecular interactions and does not employ the traditional thermodynamics, thus avoiding such a controversial notion as the surface tension of tiny clusters involved in nucleation. In the new kinetic theory the rate of emission of molecules by a new-phase particle is determined with the help of a mean first passage time analysis. This time is calculated by solving the single-molecule master equation for the probability distribution function of a surface layer molecule moving in a potential field created by the rest of the cluster. The new theory was developed for both liquid-to-solid and vapor-to-liquid phase transitions. In the former case the single-molecule master equation is the Fokker-Planck equation in the phase space which can be reduced to the Smoluchowski equation owing to the hierarchy of characteristic time scales. In the latter case, the starting master equation is a Fokker-Planck equation for the probability distribution function of a surface layer molecule with respect to both its energy and phase coordinates. Unlike the case of liquid-to-solid nucleation, this Fokker-Planck equation cannot be reduced to the Smoluchowski equation, but the hierarchy of time scales does allow one to reduce it to the Fokker-Plank equation in the energy space. The new theory provides an equation for the critical radius of a new-phase particle which in the limit of large clusters (low supersaturations) yields the Kelvin equation and hence an expression for the macroscopic surface tension. The theory was illustrated with numerical calculations for a molecular pair interaction potential combining the dispersive attraction with the hard-sphere repulsion. The results for the liquid-to-solid nucleation clearly show that at given supersaturation the nucleation rate depends on the cluster structure (for three cluster structures considered-amorphous, fcc, and icosahedral). For both the liquid-to-solid and vapor-to-liquid nucleation, the predictions of the theory are consistent with the results of classical nucleation theory (CNT) in the limit of large critical clusters (low supersaturations). For small critical clusters the new theory provides higher nucleation rates than CNT. This can be accounted for by the fact that CNT uses the macroscopic interfacial tension which presumably overpredicts the surface tension of small clusters, and hence underpredicts nucleation rates.

Specific modification of polysulfone with cluster bombardment with assistance of Ar ion irradiation

NASA Astrophysics Data System (ADS)

Xu, Guochun; Hibino, Y.; Awazu, K.; Tanihara, M.; Imanishi, Y.

2000-02-01

Objective: To develop a rapid method for the modification of polysulfone with ammonium sulfamate with the assistance of Ar ion irradiation with a multi-source cluster deposition apparatus. These surfaces mimicking the structure of heparin, a bioactive molecule, have a high anti-thrombosis property. Experimental Design: Polysulfone film, setting on a turning holder, was irradiated by Ar ions during bombardment with ammonium sulfamate clusters. The Ar ion source serves for the activation of a polymer surface and a cluster ion source supplies ammonium sulfamate molecules to react with the activated surface. After thorough washing with de-ionized sterile water, the modified surfaces were evaluated in terms of the contact angle of water, elemental composition, and binding state on electron spectroscopy for chemical analysis and platelet adhesion with platelet rich plasma. Results: The modification of polysulfone decreased the contact angle of water on surfaces from 82.6 ° down to 34.5 °. Ammonium, amine, sulfate, and thiophene combinations were formed on the modified surfaces. The adhesion numbers of the platelet were decreased to one tenth compared to the original surface. The same process was also applied to other polymers such as polyethylene, polypropylene, and polystyrene and similar outcomes were also observed. Conclusion: The primary studies showed successful modification of polysulfone with ammonium sulfamate with the assistance of Ar ion irradiation. Since the same concept can also be applied to other materials with various substrates, combined with the features of no solvent and no topographic changes, this method might be developed into a promising way for modification of polymeric materials.

Appearance and distribution of surface proteins of the human erythrocyte membrane. An electron microscope and immunochemical labeling study

PubMed Central

Shotton, D.; Thompson, K.; Wofsy, L.; Branton, D.

1978-01-01

We have used freeze-etching, before and after immunoferritin labeling, to visualize spectrin molecules and other surface proteins of the human erythrocyte membrane. After intramembrane particle aggregation was induced, spectrin molecules, identified by labeling with ferritin-conjugated antispectrin, were clustered on the cytoplasmic surface of the membrane in patches directly underlying the particle clusters. This labeling pattern confirms the involvement of spectrin in such particle aggregates, as previously inferred from indirect evidence. Ferritin-conjugated antihapten molecules, directed against external and cytoplasmic surface proteins of the erythrocyte membrane which had been covalently labeled nonspecifically with the hapten p-diazoniumphenyl-beta-D-lactoside, were similarly found in direct association with such intramembrane particle aggregates. This indicates that when spectrin and the intramembrane particles are aggregated, all the major proteins of the erythrocyte membrane are constrained to coaggregate with them. Although giving no direct information concerning the freedom of translational movement of proteins in the unperturbed erythrocyte membrane, these experiments suggest that a close dynamic association may exist between the integral and peripheral protein components of the membrane, such that immobilization of one component can restrict the lateral mobility of others. PMID:10605454

Magnetic memory of a single-molecule quantum magnet wired to a gold surface.

PubMed

Mannini, Matteo; Pineider, Francesco; Sainctavit, Philippe; Danieli, Chiara; Otero, Edwige; Sciancalepore, Corrado; Talarico, Anna Maria; Arrio, Marie-Anne; Cornia, Andrea; Gatteschi, Dante; Sessoli, Roberta

2009-03-01

In the field of molecular spintronics, the use of magnetic molecules for information technology is a main target and the observation of magnetic hysteresis on individual molecules organized on surfaces is a necessary step to develop molecular memory arrays. Although simple paramagnetic molecules can show surface-induced magnetic ordering and hysteresis when deposited on ferromagnetic surfaces, information storage at the molecular level requires molecules exhibiting an intrinsic remnant magnetization, like the so-called single-molecule magnets (SMMs). These have been intensively investigated for their rich quantum behaviour but no magnetic hysteresis has been so far reported for monolayers of SMMs on various non-magnetic substrates, most probably owing to the chemical instability of clusters on surfaces. Using X-ray absorption spectroscopy and X-ray magnetic circular dichroism synchrotron-based techniques, pushed to the limits in sensitivity and operated at sub-kelvin temperatures, we have now found that robust, tailor-made Fe(4) complexes retain magnetic hysteresis at gold surfaces. Our results demonstrate that isolated SMMs can be used for storing information. The road is now open to address individual molecules wired to a conducting surface in their blocked magnetization state, thereby enabling investigation of the elementary interactions between electron transport and magnetism degrees of freedom at the molecular scale.

Surface enhanced Raman scattering activity of dual-functional Fe3O4/Au composites

NASA Astrophysics Data System (ADS)

Wang, Li-Ping; Huang, Yu-Bin; Lai, Ying-Huang

2018-03-01

There is a high demand for multifunctional materials that can integrate sample collection and sensing. In this study, magnetic Fe3O4 clusters were fabricated using a simple solvent-thermal method. The effect of the reductant (sodium citrate, SC) on the structure and morphology of Fe3O4 was examined by the variation in the reagent amount. The resulting Fe3O4 clusters were functionalized with 3-aminopropyltriethoxysilane (APTES) to anchor Au nanoparticles to its surface. The fabricated composites were characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM), and a superconducting quantum interference device (SQUID) magnetometer. Dual-functional Fe3O4/Au clusters were obtained, effectively combining magnetic and plasmonic optical properties. The magnetic Fe3O4 cluster cores permitted the adsorption of the probe molecules, while sample concentration and collection were carried out under an external magnetic field. In addition, 4-nitrothiophenol (4-NTP) was chosen as the probe molecule to examine the analyte concentration ability and surface-enhanced Raman scattering (SERS) activity of the Fe3O4/Au composites. The results indicated that the Fe3O4/Au clusters exhibit a prominent SERS effect. The best 4-NTP detection limit obtained was 1 × 10-8 M, with a corresponding SERS analytical enhancement factor (AEF) exceeding 2 × 105.

A role for surface hydrophobicity in protein-protein recognition.

PubMed Central

Young, L.; Jernigan, R. L.; Covell, D. G.

1994-01-01

The role of hydrophobicity as a determinant of protein-protein interactions is examined. Surfaces of apo-protein targets comprising 9 classes of enzymes, 7 antibody fragments, hirudin, growth hormone, and retinol-binding protein, and their associated ligands with available X-ray structures for their complexed forms, are scanned to determine clusters of surface-accessible amino acids. Clusters of surface residues are ranked on the basis of the hydrophobicity of their constituent amino acids. The results indicate that the location of the co-crystallized ligand is commonly found to correspond with one of the strongest hydrophobic clusters on the surface of the target molecule. In 25 of 38 cases, the correspondence is exact, with the position of the most hydrophobic cluster coinciding with more than one-third of the surface buried by the bound ligand. The remaining 13 cases demonstrate this correspondence within the top 6 hydrophobic clusters. These results suggest that surface hydrophobicity can be used to identify regions of a protein's surface most likely to interact with a binding ligand. This fast and simple procedure may be useful for identifying small sets of well-defined loci for possible ligand attachment. PMID:8061602

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

PubMed

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.

Experimental methods of molecular matter-wave optics.

PubMed

Juffmann, Thomas; Ulbricht, Hendrik; Arndt, Markus

2013-08-01

We describe the state of the art in preparing, manipulating and detecting coherent molecular matter. We focus on experimental methods for handling the quantum motion of compound systems from diatomic molecules to clusters or biomolecules.Molecular quantum optics offers many challenges and innovative prospects: already the combination of two atoms into one molecule takes several well-established methods from atomic physics, such as for instance laser cooling, to their limits. The enormous internal complexity that arises when hundreds or thousands of atoms are bound in a single organic molecule, cluster or nanocrystal provides a richness that can only be tackled by combining methods from atomic physics, chemistry, cluster physics, nanotechnology and the life sciences.We review various molecular beam sources and their suitability for matter-wave experiments. We discuss numerous molecular detection schemes and give an overview over diffraction and interference experiments that have already been performed with molecules or clusters.Applications of de Broglie studies with composite systems range from fundamental tests of physics up to quantum-enhanced metrology in physical chemistry, biophysics and the surface sciences.Nanoparticle quantum optics is a growing field, which will intrigue researchers still for many years to come. This review can, therefore, only be a snapshot of a very dynamical process.

Quantum chemical analysis of thermodynamics of 2D cluster formation of alkanes at the water/vapor interface in the presence of aliphatic alcohols.

PubMed

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 essential and different for various types of amphiphilic compounds. The energetic preference of the film formation of both types depends significantly on the chain length of compounds. The surfactant concentration (in the range of X = 0-10%) exerts a slight influence on the process of film formation.

Infrared detection of (H 2O) 20 isomers of exceptional stability: A drop-like and a face-sharing pentagonal prism cluster

DOE PAGES

Pradzynski, Christoph C.; Dierking, Christoph W.; Zurheide, Florian; ...

2014-09-01

Water clusters containing fully coordinated water molecules are model systems that mimic the local environment of the condensed phase. Present knowledge about the water cluster size regime in which the transition from the allsurface to the fully solvated water molecules occurs is mainly based on theoretical predictions in lieu of the absence of precisely size resolved experimental measurements. Here, we report size and isomer selective infrared (IR) spectra of (H 2O) 20 clusters tagged with a sodium atom by employing IR excitation modulated photoionization spectroscopy. The observed absorption patterns in the OH stretching ”fingerprint” region are consistent with the theoreticallymore » predicted spectra of two structurally distinct isomers: A drop-like cluster with a fully coordinated (interior) water and an edge-sharing pentagonal prism cluster in which all atoms are on the surface. The observed isomers show exceptional stability and are predicted to be nearly isoenergetic.« less

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

PubMed

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.

Structure, reactivity, and electronic properties of V-doped Co clusters

NASA Astrophysics Data System (ADS)

Datta, Soumendu; Kabir, Mukul; Saha-Dasgupta, Tanusri; Mookerjee, Abhijit

2009-08-01

Structures and physicochemical properties of V-doped Co13 clusters have been studied in detail using density-functional-theory-based first-principles method. We have found anomalous variation in stability of the doped clusters with increasing V concentration, which has been nicely demonstrated in terms of energetics and electronic properties of the clusters. Our study explains the nonmonotonic variation in reactivity of Co13-mVm clusters toward H2 molecules as reported experimentally [Nonose , J. Phys. Chem. 94, 2744 (1990)]. Moreover, it provides useful insight into the cluster geometry and chemically active sites on the cluster surface, which can help to design better catalytic processes.

Measuring the reactivity of a silicon-terminated probe

NASA Astrophysics Data System (ADS)

Sweetman, Adam; Stirling, Julian; Jarvis, Samuel Paul; Rahe, Philipp; Moriarty, Philip

2016-09-01

It is generally accepted that the exposed surfaces of silicon crystals are highly reactive due to the dangling bonds which protrude into the vacuum. However, surface reconstruction not only modifies the reactivity of bulk silicon crystals, but also plays a key role in determining the properties of silicon nanocrystals. In this study we probe the reactivity of silicon clusters at the end of a scanning probe tip by examining their interaction with closed-shell fullerene molecules. Counter to intuitive expectations, many silicon clusters do not react strongly with the fullerene cage, and we find that only specific highly oriented clusters have sufficient reactivity to break open the existing carbon-carbon bonds.

GPI-anchored GFP signals Ca2+ but is homogeneously distributed on the cell surface.

PubMed

Hiscox, Stephen; Hallett, Maurice B; Morgan, B Paul; van den Berg, Carmen W

2002-05-03

Glycosyl-phosphatidylinositol (GPI)-anchored proteins are unique in that they penetrate only the outer leaflet of the plasma membrane but are still able to mediate intracellular signalling events following antibody-induced ligation. Detergent solubilisation studies suggest that microdomains exist at the cell surface within which are sequestered GPI-linked proteins. Here we report the construction and expression of a fluorescent GPI anchor on the surface of CHO, EL4, and U937 cells by fusing green fluorescent protein (GFP) to the GPI-attachment site of CD59. The resultant GFP-GPI has properties comparable to that of endogenously expressed GPI-anchored molecules as shown by Triton X-114 partitioning. However, sucrose gradient floatation showed that GFP-GPI was only partially resistant to detergent solubilisation. Furthermore confocal scanning laser microscopy revealed a homogeneous distribution of GFP-GPI at the cell surface, which only became clustered following cross-linking of the GPI anchor via an anti-GFP antibody. Surprisingly, GFP-GPI signalled Ca2+ change upon cross-linking demonstrating its signalling competence. Our results suggest that the GPI-anchor itself does not confer a clustered distribution to molecules but that clustering occurs following ligation with antibody, which allows the protein to become Ca2+ signalling competent. Copyright 2002 Elsevier Science (USA).

Stabilizing subnanometer Ag(0) nanoclusters by thiolate and diphosphine ligands and their crystal structures

NASA Astrophysics Data System (ADS)

Yang, Huayan; Wang, Yu; Zheng, Nanfeng

2013-03-01

The combined use of thiolate and diphosphine as surface ligands helps to stabilize subnanometer Ag(0) nanoclusters, resulting in the successful crystallization of two Ag(0)-containing nanoclusters (Ag16 and Ag32) for X-ray single crystal analysis. Both clusters have core-shell structures with Ag86+ and Ag2212+ as their cores, which are not simply either fragments of face-centered cubic metals or their five-fold twinned counterparts. The clusters display UV-Vis absorption spectra consisting of molecule-like optical transitions.The combined use of thiolate and diphosphine as surface ligands helps to stabilize subnanometer Ag(0) nanoclusters, resulting in the successful crystallization of two Ag(0)-containing nanoclusters (Ag16 and Ag32) for X-ray single crystal analysis. Both clusters have core-shell structures with Ag86+ and Ag2212+ as their cores, which are not simply either fragments of face-centered cubic metals or their five-fold twinned counterparts. The clusters display UV-Vis absorption spectra consisting of molecule-like optical transitions. Electronic supplementary information (ESI) available: Experimental details, more pictures of the structure and XPS spectra of the clusters. CCDC 916463 and 916464. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c3nr34328f

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

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

Stein, Tamar; Bandyopadhyay, Biswajit; Troy, Tyler P.

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 (Cmore » 2H 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 4H 4 + and C 6H 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 2H 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 6H 6 + isomers. Lastly, these results suggest a path for aromatic ring formation in cold acetylene-rich environments such as parts of the ISM.« less

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

PubMed Central

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

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

PubMed

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

DOE PAGES

Stein, Tamar; Bandyopadhyay, Biswajit; Troy, Tyler P.; ...

2017-05-08

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 (Cmore » 2H 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 4H 4 + and C 6H 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 2H 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 6H 6 + isomers. Lastly, these results suggest a path for aromatic ring formation in cold acetylene-rich environments such as parts of the ISM.« less

Theoretical studies on the coupling interactions in H2SO4···HOO˙···(H2O)n (n = 0-2) clusters: toward understanding the role of water molecules in the uptake of HOO˙ radical by sulfuric acid aerosols.

PubMed

Li, Ping; Ma, Zhiying; Wang, Weihua; Zhai, Yazhou; Sun, Haitao; Bi, Siwei; Bu, Yuxiang

2011-01-21

A detailed knowledge of coupling interactions among sulfuric acid (H(2)SO(4)), the hydroperoxyl radical (HOO˙), and water molecules (H(2)O) is crucial for the better understanding of the uptake of HOO˙ radicals by sulfuric acid aerosols at different atmospheric humidities. In the present study, the equilibrium structures, binding energies, equilibrium distributions, and the nature of the coupling interactions in H(2)SO(4)···HOO˙···(H(2)O)(n) (n = 0-2) clusters have been systematically investigated at the B3LYP/6-311++G(3df,3pd) level of theory in combination with the atoms in molecules (AIM) theory, natural bond orbital (NBO) method, energy decomposition analyses, and ab initio molecular dynamics. Two binary, five ternary, and twelve tetramer clusters possessing multiple intermolecular H-bonds have been located on their potential energy surfaces. Two different modes for water molecules have been observed to influence the coupling interactions between H(2)SO(4) and HOO˙ through the formations of intermolecular H-bonds with or without breaking the original intermolecular H-bonds in the binary H(2)SO(4)···HOO˙ cluster. It was found that the introduction of one or two water molecules can efficiently enhance the interactions between H(2)SO(4) and HOO˙, implying the positive role of water molecules in the uptake of the HOO˙ radical by sulfuric acid aerosols. Additionally, the coupling interaction modes of the most stable clusters under study have been verified by the ab initio molecular dynamics.

Dynamic structural disorder in supported nanoscale catalysts

NASA Astrophysics Data System (ADS)

Rehr, J. J.; Vila, F. D.

2014-04-01

We investigate the origin and physical effects of "dynamic structural disorder" (DSD) in supported nano-scale catalysts. DSD refers to the intrinsic fluctuating, inhomogeneous structure of such nano-scale systems. In contrast to bulk materials, nano-scale systems exhibit substantial fluctuations in structure, charge, temperature, and other quantities, as well as large surface effects. The DSD is driven largely by the stochastic librational motion of the center of mass and fluxional bonding at the nanoparticle surface due to thermal coupling with the substrate. Our approach for calculating and understanding DSD is based on a combination of real-time density functional theory/molecular dynamics simulations, transient coupled-oscillator models, and statistical mechanics. This approach treats thermal and dynamic effects over multiple time-scales, and includes bond-stretching and -bending vibrations, and transient tethering to the substrate at longer ps time-scales. Potential effects on the catalytic properties of these clusters are briefly explored. Model calculations of molecule-cluster interactions and molecular dissociation reaction paths are presented in which the reactant molecules are adsorbed on the surface of dynamically sampled clusters. This model suggests that DSD can affect both the prefactors and distribution of energy barriers in reaction rates, and thus can significantly affect catalytic activity at the nano-scale.

Symmetry-Based Techniques for Qualitative Understanding of Rovibrational Effects in Spherical-Top Molecular Spectra and Dynamics

NASA Astrophysics Data System (ADS)

Mitchell, Justin Chadwick

2011-12-01

Using light to probe the structure of matter is as natural as opening our eyes. Modern physics and chemistry have turned this art into a rich science, measuring the delicate interactions possible at the molecular level. Perhaps the most commonly used tool in computational spectroscopy is that of matrix diagonalization. While this is invaluable for calculating everything from molecular structure and energy levels to dipole moments and dynamics, the process of numerical diagonalization is an opaque one. This work applies symmetry and semi-classical techniques to elucidate numerical spectral analysis for high-symmetry molecules. Semi-classical techniques, such as the Potential Energy Surfaces, have long been used to help understand molecular vibronic and rovibronic spectra and dynamics. This investigation focuses on newer semi-classical techniques that apply Rotational Energy Surfaces (RES) to rotational energy level clustering effects in high-symmetry molecules. Such clusters exist in rigid rotor molecules as well as deformable spherical tops. This study begins by using the simplicity of rigid symmetric top molecules to clarify the classical-quantum correspondence of RES semi-classical analysis and then extends it to a more precise and complete theory of modern high-resolution spectra. RES analysis is extended to molecules having more complex and higher rank tensorial rotational and rovibrational Hamiltonians than were possible to understand before. Such molecules are shown to produce an extraordinary range of rotational level clusters, corresponding to a panoply of symmetries ranging from C4v to C2 and C1 (no symmetry) with a corresponding range of new angular momentum localization and J-tunneling effects. Using RES topography analysis and the commutation duality relations between symmetry group operators in the lab-frame to those in the body-frame, it is shown how to better describe and catalog complex splittings found in rotational level clusters. Symmetry character analysis is generalized to give analytic eigensolutions. An appendix provides vibrational analogies. For the first time, interactions between molecular vibrations (polyads) are described semi-classically by multiple RES. This is done for the nu 3/2nu4 dyad of CF4. The nine-surface RES topology of the U(9)-dyad agrees with both computational and experimental work. A connection between this and a simpler U(2) example is detailed in an Appendix.

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

PubMed

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.

Self-organized molecular films with long-range quasiperiodic order.

PubMed

Fournée, Vincent; Gaudry, Émilie; Ledieu, Julian; de Weerd, Marie-Cécile; Wu, Dongmei; Lograsso, Thomas

2014-04-22

Self-organized molecular films with long-range quasiperiodic order have been grown by using the complex potential energy landscape of quasicrystalline surfaces as templates. The long-range order arises from a specific subset of quasilattice sites acting as preferred adsorption sites for the molecules, thus enforcing a quasiperiodic structure in the film. These adsorption sites exhibit a local 5-fold symmetry resulting from the cut by the surface plane through the cluster units identified in the bulk solid. Symmetry matching between the C60 fullerene and the substrate leads to a preferred adsorption configuration of the molecules with a pentagonal face down, a feature unique to quasicrystalline surfaces, enabling efficient chemical bonding at the molecule-substrate interface. This finding offers opportunities to investigate the physical properties of model 2D quasiperiodic systems, as the molecules can be functionalized to yield architectures with tailor-made properties.

Novel SERS materials for multiplex biomolecular detection via controlled nanoparticle linking and polymer encapsulation

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

Braun, G B; Lee, S J; Laurence, T

2008-07-21

Over the past decade the emphasis on single-molecule sensitivity of surface-enhanced Raman spectroscopy (SERS) has brought to prominence the special role played by so-called SERS 'hot spots', oftentimes nanometer-scale junctions between nanostructures. In this report, optimally SERS enhancing silver clusters were synthesized using bifunctional linkers and polymer and/or protein encapsulation. The synthesis, which results in stable clusters even when stored for months or dried and re-dissolved, is scalable to large quantities. Using a sacrificial linker approach we also employ a permeable polymer/protein shell for general small molecule sensing. Finally, we utilize these nanomaterials by tagging specific epitopes on cancer cellsmore » and show that SERS signals from single clusters can be measured routinely.« less

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

NASA Astrophysics Data System (ADS)

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.

DNA-Mediated Patterning of Single Quantum Dot Nanoarrays: A Reusable Platform for Single-Molecule Control

NASA Astrophysics Data System (ADS)

Huang, Da; Freeley, Mark; Palma, Matteo

2017-03-01

We present a facile strategy of general applicability for the assembly of individual nanoscale moieties in array configurations with single-molecule control. Combining the programming ability of DNA as a scaffolding material with a one-step lithographic process, we demonstrate the patterning of single quantum dots (QDs) at predefined locations on silicon and transparent glass surfaces: as proof of concept, clusters of either one, two, or three QDs were assembled in highly uniform arrays with a 60 nm interdot spacing within each cluster. Notably, the platform developed is reusable after a simple cleaning process and can be designed to exhibit different geometrical arrangements.

Reaction Rate of Small Diffusing Molecules on a Cylindrical Membrane

NASA Astrophysics Data System (ADS)

Straube, Ronny; Ward, Michael J.; Falcke, Martin

2007-10-01

Biomembranes consist of a lipid bi-layer into which proteins are embedded to fulfill numerous tasks in localized regions of the membrane. Often, the proteins have to reach these regions by simple diffusion. Motivated by the observation that IP3 receptor channels (IP3R) form clusters on the surface of the endoplasmic reticulum (ER) during ATP-induced calcium release, the reaction rate of small diffusing molecules on a cylindrical membrane is calculated based on the Smoluchowski approach. In this way, the cylindrical topology of the tubular ER is explicitly taken into account. The problem can be reduced to the solution of the diffusion equation on a finite cylindrical surface containing a small absorbing hole. The solution is constructed by matching appropriate `inner' and `outer' asymptotic expansions. The asymptotic results are compared with those from numerical simulations and excellent agreement is obtained. For realistic parameter sets, we find reaction rates in the range of experimentally measured clustering rates of IP3R. This supports the idea that clusters are formed by a purely diffusion limited process.

Acetonitrile cluster solvation in a cryogenic ethane-methane-propane liquid: Implications for Titan lake chemistry.

PubMed

Corrales, L René; Yi, Thomas D; Trumbo, Samantha K; Shalloway, David; Lunine, Jonathan I; Usher, David A

2017-03-14

The atmosphere of Titan, Saturn's largest moon, exhibits interesting UV- and radiation-driven chemistry between nitrogen and methane, resulting in dipolar, nitrile-containing molecules. The assembly and subsequent solvation of such molecules in the alkane lakes and seas found on the moon's surface are of particular interest for investigating the possibility of prebiotic chemistry in Titan's hydrophobic seas. Here we characterize the solvation of acetonitrile, a product of Titan's atmospheric radiation chemistry tentatively detected on Titan's surface [H. B. Niemann et al., Nature 438, 779-784 (2005)], in an alkane mixture estimated to match a postulated composition of the smaller lakes during cycles of active drying and rewetting. Molecular dynamics simulations are employed to determine the potential of mean force of acetonitrile (CH 3 CN) clusters moving from the alkane vapor into the bulk liquid. We find that the clusters prefer the alkane liquid to the vapor and do not dissociate in the bulk liquid. This opens up the possibility that acetonitrile-based microscopic polar chemistry may be possible in the otherwise nonpolar Titan lakes.

Coverage dependent molecular assembly of anthraquinone on Au(111)

NASA Astrophysics Data System (ADS)

DeLoach, Andrew S.; Conrad, Brad R.; Einstein, T. L.; Dougherty, Daniel B.

2017-11-01

A scanning tunneling microscopy study of anthraquinone (AQ) on the Au(111) surface shows that the molecules self-assemble into several structures depending on the local surface coverage. At high coverages, a close-packed saturated monolayer is observed, while at low coverages, mobile surface molecules coexist with stable chiral hexamer clusters. At intermediate coverages, a disordered 2D porous network interlinking close-packed islands is observed in contrast to the giant honeycomb networks observed for the same molecule on Cu(111). This difference verifies the predicted extreme sensitivity [J. Wyrick et al., Nano Lett. 11, 2944 (2011)] of the pore network to small changes in the surface electronic structure. Quantitative analysis of the 2D pore network reveals that the areas of the vacancy islands are distributed log-normally. Log-normal distributions are typically associated with the product of random variables (multiplicative noise), and we propose that the distribution of pore sizes for AQ on Au(111) originates from random linear rate constants for molecules to either desorb from the surface or detach from the region of a nucleated pore.

Coverage dependent molecular assembly of anthraquinone on Au(111).

PubMed

DeLoach, Andrew S; Conrad, Brad R; Einstein, T L; Dougherty, Daniel B

2017-11-14

A scanning tunneling microscopy study of anthraquinone (AQ) on the Au(111) surface shows that the molecules self-assemble into several structures depending on the local surface coverage. At high coverages, a close-packed saturated monolayer is observed, while at low coverages, mobile surface molecules coexist with stable chiral hexamer clusters. At intermediate coverages, a disordered 2D porous network interlinking close-packed islands is observed in contrast to the giant honeycomb networks observed for the same molecule on Cu(111). This difference verifies the predicted extreme sensitivity [J. Wyrick et al., Nano Lett. 11, 2944 (2011)] of the pore network to small changes in the surface electronic structure. Quantitative analysis of the 2D pore network reveals that the areas of the vacancy islands are distributed log-normally. Log-normal distributions are typically associated with the product of random variables (multiplicative noise), and we propose that the distribution of pore sizes for AQ on Au(111) originates from random linear rate constants for molecules to either desorb from the surface or detach from the region of a nucleated pore.

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

Laskin, Julia; Johnson, Grant E.; Prabhakaran, Venkateshkumar

Immobilization of complex molecules and clusters on supports plays an important role in a variety of disciplines including materials science, catalysis and biochemistry. In particular, deposition of clusters on surfaces has attracted considerable attention due to their non-scalable, highly size-dependent properties. The ability to precisely control the composition and morphology of clusters and small nanoparticles on surfaces is crucial for the development of next generation materials with rationally tailored properties. Soft- and reactive landing of ions onto solid or liquid surfaces introduces unprecedented selectivity into surface modification by completely eliminating the effect of solvent and sample contamination on the qualitymore » of the film. The ability to select the mass-to-charge ratio of the precursor ion, its kinetic energy and charge state along with precise control of the size, shape and position of the ion beam on the deposition target makes soft-landing an attractive approach for surface modification. High-purity uniform thin films on surfaces generated using mass-selected ion deposition facilitate understanding of critical interfacial phenomena relevant to catalysis, energy generation and storage, and materials science. Our efforts have been directed toward understanding charge retention by soft-landed metal and metal-oxide cluster ions, which may affect both their structure and reactivity. Specifically, we have examined the effect of the surface on charge retention by both positively and negatively charged cluster ions. We found that the electronic properties of the surface play an important role in charge retention by cluster cations. Meanwhile, the electron binding energy is a key factor determining charge retention by cluster anions. These findings provide the scientific foundation for the rational design of interfaces for advanced catalysts and energy storage devices. Further optimization of electrode-electrolyte interfaces for applications in energy storage and electrocatalysis may be achieved by understanding and controlling the properties of soft-landed cluster ions.« less

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

NASA Astrophysics Data System (ADS)

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.

First principles DFT study of dye-sensitized CdS quantum dots

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

Jain, Kalpna; Singh, Kh. S.; Kishor, Shyam, E-mail: shyam387@gmail.com

2014-04-24

Dye-sensitized quantum dots (QDs) are considered promising candidates for dye-sensitized solar cells. In order to maximize their efficiency, detailed theoretical studies are important. Here, we report a first principles density functional theory (DFT) investigation of experimentally realized dye - sensitized QD / ligand systems, viz., Cd{sub 16}S{sub 16}, capped with acetate molecules and a coumarin dye. The hybrid B3LYP functional and a 6−311+G(d,p)/LANL2dz basis set are used to study the geometric, energetic and electronic properties of these clusters. There is significant structural rearrangement in all the clusters studied - on the surface for the bare QD, and in the positionsmore » of the acetate / dye ligands for the ligated QDs. The density of states (DOS) of the bare QD shows states in the band gap, which disappear on surface passivation with the acetate molecules. Interestingly, in the dye-sensitised QD, the HOMO is found to be localized mainly on the dye molecule, while the LUMO is on the QD, as required for photo-induced electron injection from the dye to the QD.« less

Robust nonparametric quantification of clustering density of molecules in single-molecule localization microscopy

PubMed Central

Jiang, Shenghang; Park, Seongjin; Challapalli, Sai Divya; Fei, Jingyi; Wang, Yong

2017-01-01

We report a robust nonparametric descriptor, J′(r), for quantifying the density of clustering molecules in single-molecule localization microscopy. J′(r), based on nearest neighbor distribution functions, does not require any parameter as an input for analyzing point patterns. We show that J′(r) displays a valley shape in the presence of clusters of molecules, and the characteristics of the valley reliably report the clustering features in the data. Most importantly, the position of the J′(r) valley (rJm′) depends exclusively on the density of clustering molecules (ρc). Therefore, it is ideal for direct estimation of the clustering density of molecules in single-molecule localization microscopy. As an example, this descriptor was applied to estimate the clustering density of ptsG mRNA in E. coli bacteria. PMID:28636661

Quantum mechanics capacitance molecular mechanics modeling of core-electron binding energies of methanol and methyl nitrite on Ag(111) surface.

PubMed

Löytynoja, T; Li, X; Jänkälä, K; Rinkevicius, Z; Ågren, H

2016-07-14

We study a newly devised quantum mechanics capacitance molecular mechanics (QMCMM) method for the calculation of core-electron binding energies in the case of molecules adsorbed on metal surfaces. This yet untested methodology is applied to systems with monolayer of methanol/methyl nitrite on an Ag(111) surface at 100 K temperature. It was found out that the studied C, N, and O 1s core-hole energies converge very slowly as a function of the radius of the metallic cluster, which was ascribed to build up of positive charge on the edge of the Ag slab. Further analysis revealed that an extrapolation process can be used to obtain binding energies that deviated less than 0.5 eV against experiments, except in the case of methanol O 1s where the difference was as large as 1.8 eV. Additional QM-cluster calculations suggest that the latter error can be connected to the lack of charge transfer over the QM-CMM boundary. Thus, the results indicate that the QMCMM and QM-cluster methods can complement each other in a holistic picture of molecule-adsorbate core-ionization studies, where all types of intermolecular interactions are considered.

Quantum mechanics capacitance molecular mechanics modeling of core-electron binding energies of methanol and methyl nitrite on Ag(111) surface

NASA Astrophysics Data System (ADS)

Löytynoja, T.; Li, X.; Jänkälä, K.; Rinkevicius, Z.; Ågren, H.

2016-07-01

We study a newly devised quantum mechanics capacitance molecular mechanics (QMCMM) method for the calculation of core-electron binding energies in the case of molecules adsorbed on metal surfaces. This yet untested methodology is applied to systems with monolayer of methanol/methyl nitrite on an Ag(111) surface at 100 K temperature. It was found out that the studied C, N, and O 1s core-hole energies converge very slowly as a function of the radius of the metallic cluster, which was ascribed to build up of positive charge on the edge of the Ag slab. Further analysis revealed that an extrapolation process can be used to obtain binding energies that deviated less than 0.5 eV against experiments, except in the case of methanol O 1s where the difference was as large as 1.8 eV. Additional QM-cluster calculations suggest that the latter error can be connected to the lack of charge transfer over the QM-CMM boundary. Thus, the results indicate that the QMCMM and QM-cluster methods can complement each other in a holistic picture of molecule-adsorbate core-ionization studies, where all types of intermolecular interactions are considered.

A kinetic model for heterogeneous condensation of vapor on an insoluble spherical particle.

PubMed

Luo, Xisheng; Fan, Yu; Qin, Fenghua; Gui, Huaqiao; Liu, Jianguo

2014-01-14

A kinetic model is developed to describe the heterogeneous condensation of vapor on an insoluble spherical particle. This new model considers two mechanisms of cluster growth: direct addition of water molecules from the vapor and surface diffusion of adsorbed water molecules on the particle. The effect of line tension is also included in the model. For the first time, the exact expression of evaporation coefficient is derived for heterogeneous condensation of vapor on an insoluble spherical particle by using the detailed balance. The obtained expression of evaporation coefficient is proved to be also correct in the homogeneous condensation and the heterogeneous condensation on a planar solid surface. The contributions of the two mechanisms to heterogeneous condensation including the effect of line tension are evaluated and analysed. It is found that the cluster growth via surface diffusion of adsorbed water molecules on the particle is more important than the direct addition from the vapor. As an example of our model applications, the growth rate of the cap shaped droplet on the insoluble spherical particle is derived. Our evaluation shows that the growth rate of droplet in heterogeneous condensation is larger than that in homogeneous condensation. These results indicate that an explicit kinetic model is benefit to the study of heterogeneous condensation on an insoluble spherical particle.

DFT study of benzyl alcohol/TiO2 interfacial surface complex: reaction pathway and mechanism of visible light absorption.

PubMed

Zhao, Lei; Gu, Feng Long; Kim, Minjae; Miao, Maosheng; Zhang, Rui-Qin

2017-09-24

We propose a new pathway for the adsorption of benzyl alcohol on the surface of TiO 2 and the formation of interfacial surface complex (ISC). The reaction free energies and reaction kinetics were thoroughly investigated by density functional calculations. The TiO 2 surfaces were modeled by clusters consisting of 4 Ti atoms and 18 O atoms passivated by H, OH group and H 2 O molecules. Compared with solid-state calculations utilizing the periodicity of the materials, such cluster modeling allows inclusion of the high-order correlation effects that seem to be essential for the adsorption of organic molecules onto solid surfaces. The effects of both acidity and solvation are included in our calculations, which demonstrate that the new pathway is competitive with a previous pathway. The electronic structure calculations based on the relaxed ISC structures reveal that the chemisorption of benzyl alcohol on the TiO 2 surface greatly alters the nature of the frontier molecular orbitals. The resulted reduced energy gap in ISC matches the energy of visible light, showing how the adsorption of benzyl alcohol sensitizes the TiO 2 surface. Graphical Abstract The chemisorption of benzyl alcohol on TiO 2 surface greatly alters the nature of the frontier molecular orbitals and the formed interfacial surface complex can be sensitized by visible light.

Nanoscale Relationship Between CD4 and CD25 of T Cells Visualized with NSOM/QD-Based Dual-Color Imaging System

NASA Astrophysics Data System (ADS)

Fan, Jinping; Lu, Xiaoxu; Liu, Shengde; Zhong, Liyun

2015-10-01

In this study, by using of near-field scanning optical microscopy (NSOM)/immune-labeling quantum dot (QD)-based dual-color imaging system, we achieved the direct visualization of nanoscale profiles for distribution and organization of CD4 and CD25 molecules in T cells. A novel and interesting finding was that though CD25 clustering as nanodomains were observed on the surface of CD4+CD25high regulatory T cells, these CD25 nanodomains were not co-localized with CD4 nanodomains. This result presented that the formation of these CD25 nanodomains on the surface of CD4+CD25high T cells were not associated with the response of T cell receptor (TCR)/CD3-dependent signal transduction. In contrast, on the surface of CD4+CD25low T cells, CD25 molecules distributed randomly without forming nanodomains while CD4 clustering as nanodomains can be observed; on the surface of CD8+CD25+ T cells, CD25 clustering as nanodomains and co-localization with CD8 nanodomains were observed. Collectively, above these results exhibited that TCR/CD3-based microdomains were indeed required for TCR/CD3-mediated T cells activation and enhanced the immune activity of CD4+CD25low T cells or CD8+CD25+ T cells. In particular, it was found that the formation of CD25 nanodomains and their segregation from TCR/CD3 microdomains were the intrinsic capability of CD4+CD25high T cells, suggesting this specific imaging feature of CD25 should be greatly associated with the regulatory activity of CD4+CD25high T cells. Importantly, this novel NSOM/QD-based dual-color imaging system will provide a useful tool for the research of distribution-function relationship of cell-surface molecules.

A unifying model for adsorption and nucleation of vapors on solid surfaces.

PubMed

Laaksonen, Ari

2015-04-23

Vapor interaction with solid surfaces is traditionally described with adsorption isotherms in the undersaturated regime and with heterogeneous nucleation theory in the supersaturated regime. A class of adsorption isotherms is based on the idea of vapor molecule clustering around so-called active sites. However, as the isotherms do not account for the surface curvature effects of the clusters, they predict an infinitely thick adsorption layer at saturation and do not recognize the existence of the supersaturated regime. The classical heterogeneous nucleation theory also builds on the idea of cluster formation, but describes the interactions between the surface and the cluster with a single parameter, the contact angle, which provides limited information compared with adsorption isotherms. Here, a new model of vapor adsorption on nonporous solid surfaces is derived. The basic assumption is that adsorption proceeds via formation of molecular clusters, modeled as liquid caps. The equilibrium of the individual clusters with the vapor phase is described with the Frenkel-Halsey-Hill (FHH) adsorption theory modified with the Kelvin equation that corrects for the curvature effect on vapor pressure. The new model extends the FHH adsorption isotherm to be applicable both at submonolayer surface coverages and at supersaturated conditions. It shows good agreement with experimental adsorption data from 12 different adsorbent-adsorbate systems. The model predictions are also compared against heterogeneous nucleation data, and they show much better agreement than predictions of the classical heterogeneous nucleation theory.

Hydrophobic hydration driven self-assembly of curcumin in water: Similarities to nucleation and growth under large metastability, and an analysis of water dynamics at heterogeneous surfaces

NASA Astrophysics Data System (ADS)

Hazra, Milan Kumar; Roy, Susmita; Bagchi, Biman

2014-11-01

As the beneficial effects of curcumin have often been reported to be limited to its small concentrations, we have undertaken a study to find the aggregation properties of curcumin in water by varying the number of monomers. Our molecular dynamics simulation results show that the equilibrated structure is always an aggregated state with remarkable structural rearrangements as we vary the number of curcumin monomers from 4 to 16 monomers. We find that the curcumin monomers form clusters in a very definite pattern where they tend to aggregate both in parallel and anti-parallel orientation of the phenyl rings, often seen in the formation of β-sheet in proteins. A considerable enhancement in the population of parallel alignments is observed with increasing the system size from 12 to 16 curcumin monomers. Due to the prevalence of such parallel alignment for large system size, a more closely packed cluster is formed with maximum number of hydrophobic contacts. We also follow the pathway of cluster growth, in particular the transition from the initial segregated to the final aggregated state. We find the existence of a metastable structural intermediate involving a number of intermediate-sized clusters dispersed in the solution. We have constructed a free energy landscape of aggregation where the metatsable state has been identified. The course of aggregation bears similarity to nucleation and growth in highly metastable state. The final aggregated form remains stable with the total exclusion of water from its sequestered hydrophobic core. We also investigate water structure near the cluster surface along with their orientation. We find that water molecules form a distorted tetrahedral geometry in the 1st solvation layer of the cluster, interacting rather strongly with the hydrophilic groups at the surface of the curcumin. The dynamics of such quasi-bound water molecules near the surface of curcumin cluster is considerably slower than the bulk signifying a restricted motion as often found in protein hydration layer.

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

NASA Astrophysics Data System (ADS)

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.

On the chemical enhancement in SERS

NASA Astrophysics Data System (ADS)

Jensen, Lasse

2012-12-01

In Surface-enhanced Raman scattering (SERS), the Raman signal of a molecule adsorbed on a metal surface is enhanced by many orders of magnitude. This provides a "finger-print" of molecules which can be used in ultrasensitive sensing devises. Here we present a time-dependent density functional theory (TDDFT) study of the molecule-surface chemical coupling in SERS. A systematic study of the chemical enhancement (CHEM) of meta-and para-substituted pyridines interacting with a small silver cluster (Ag20) is presented. We find that the magnitude of chemical enhancement is governed to a large extent by the energy difference between the highest occupied energy level (HOMO) of the metal and the lowest unoccupied energy level (LUMO) of the molecule. A two-state approximation shows that the enhancement scales roughly as (ωX/ω¯e)4, where accent="true">ω¯e is an average excitation energy between the HOMO of the metal and the LUMO of the molecule and wX the HOMO-LUMO gap of the free molecule. Furthermore, we demonstrate that it is possible to control the CHEM enhancement by switching a dithienylethene photoswitch from its closed form to its open form. The open form of the photoswitch is found to be the strongest Raman scatterer when adsorbed on the surface whereas the opposite is found for the free molecule. This trend is explained using the simple two-state approximation.

Identifying Few-Molecule Water Clusters with High Precision on Au(111) Surface.

PubMed

Dong, Anning; Yan, Lei; Sun, Lihuan; Yan, Shichao; Shan, Xinyan; Guo, Yang; Meng, Sheng; Lu, Xinghua

2018-06-01

Revealing the nature of a hydrogen-bond network in water structures is one of the imperative objectives of science. With the use of a low-temperature scanning tunneling microscope, water clusters on a Au(111) surface were directly imaged with molecular resolution by a functionalized tip. The internal structures of the water clusters as well as the geometry variations with the increase of size were identified. In contrast to a buckled water hexamer predicted by previous theoretical calculations, our results present deterministic evidence for a flat configuration of water hexamers on Au(111), corroborated by density functional theory calculations with properly implemented van der Waals corrections. The consistency between the experimental observations and improved theoretical calculations not only renders the internal structures of absorbed water clusters unambiguously, but also directly manifests the crucial role of van der Waals interactions in constructing water-solid interfaces.

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

Löytynoja, T., E-mail: tuomas.loytynoja@oulu.fi; Division of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, SE-106 91 Stockholm; Li, X.

We study a newly devised quantum mechanics capacitance molecular mechanics (QMCMM) method for the calculation of core-electron binding energies in the case of molecules adsorbed on metal surfaces. This yet untested methodology is applied to systems with monolayer of methanol/methyl nitrite on an Ag(111) surface at 100 K temperature. It was found out that the studied C, N, and O 1s core-hole energies converge very slowly as a function of the radius of the metallic cluster, which was ascribed to build up of positive charge on the edge of the Ag slab. Further analysis revealed that an extrapolation process canmore » be used to obtain binding energies that deviated less than 0.5 eV against experiments, except in the case of methanol O 1s where the difference was as large as 1.8 eV. Additional QM-cluster calculations suggest that the latter error can be connected to the lack of charge transfer over the QM–CMM boundary. Thus, the results indicate that the QMCMM and QM-cluster methods can complement each other in a holistic picture of molecule-adsorbate core-ionization studies, where all types of intermolecular interactions are considered.« less

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

NASA Astrophysics Data System (ADS)

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.

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

Petit, Chad M.; Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803; Chouljenko, Vladimir N.

The SARS-coronavirus (SARS-CoV) is the etiological agent of the severe acute respiratory syndrome (SARS). The SARS-CoV spike (S) glycoprotein mediates membrane fusion events during virus entry and virus-induced cell-to-cell fusion. The cytoplasmic portion of the S glycoprotein contains four cysteine-rich amino acid clusters. Individual cysteine clusters were altered via cysteine-to-alanine amino acid replacement and the modified S glycoproteins were tested for their transport to cell-surfaces and ability to cause cell fusion in transient transfection assays. Mutagenesis of the cysteine cluster I, located immediately proximal to the predicted transmembrane, domain did not appreciably reduce cell-surface expression, although S-mediated cell fusion wasmore » reduced by more than 50% in comparison to the wild-type S. Similarly, mutagenesis of the cysteine cluster II located adjacent to cluster I reduced S-mediated cell fusion by more than 60% compared to the wild-type S, while cell-surface expression was reduced by less than 20%. Mutagenesis of cysteine clusters III and IV did not appreciably affect S cell-surface expression or S-mediated cell fusion. The wild-type S was palmitoylated as evidenced by the efficient incorporation of {sup 3}H-palmitic acid in wild-type S molecules. S glycoprotein palmitoylation was significantly reduced for mutant glycoproteins having cluster I and II cysteine changes, but was largely unaffected for cysteine cluster III and IV mutants. These results show that the S cytoplasmic domain is palmitoylated and that palmitoylation of the membrane proximal cysteine clusters I and II may be important for S-mediated cell fusion.« less

PREFACE: International Conference on Many Particle Spectroscopy of Atoms, Molecules, Clusters and Surfaces (MPS2014)

NASA Astrophysics Data System (ADS)

Ancarani, Lorenzo Ugo

2015-04-01

This volume contains a collection of contributions from the invited speakers at the 2014 edition of the International Conference on Many Particle Spectroscopy of Atoms, Molecules, Clusters and Surfaces held in Metz, France, from 15th to 18th July 2014. This biennial conference alternates with the ICPEAC satellite International Symposium on (e,2e), Double Photoionization and Related Topics, and is concerned with experimental and theoretical studies of radiation interactions with matter. These include many-body and electron-electron correlation effects in excitation, and in single and multiple ionization of atoms, molecules, clusters and surfaces with various projectiles: electrons, photons and ions. More than 80 scientists, from 19 different countries around the world, came together to discuss the most recent progress on these topics. The scientific programme included 28 invited talks and a poster session extending over the three days of the meeting. Amongst the 51 posters, 11 have been selected and were advertised through short talks. Besides, Professor Nora Berrah gave a talk in memory of Professor Uwe Becker who sadly passed away shortly after co-chairing the previous edition of this conference. Financial support from the Institut Jean Barriol, Laboratoire SRSMC, Groupement de Recherche THEMS (CNRS), Ville de Metz, Metz Métropole, Conseil Général de la Moselle and Région Lorraine is gratefully acknowledged. Finally, I would like to thank the members of the local committee and the staff of the Université de Lorraine for making the conference run smoothly, the International Advisory Board for building up the scientific programme, the sessions chairpersons, those who gave their valuable time in carefully refereeing the articles of this volume and last, but not least, all participants for contributing to lively and fruitful discussions throughout the meeting.

Modulation of sickle cell crisis by naturally occurring band 3 specific antibodies -- a malaria link.

PubMed

Kennedy, James Randall

2002-05-01

This paper's focus is prevention of sickle cell adhesion resulting from the erythrocyte's prematurely denatured hemoglobin. This denatured hemoglobin causes a molecule called band 3 to cluster on the erythrocyte's surface and adhere to the CD36 molecule located on the microvascular endothelium. Natural antibodies recognize these clusters on senescent erythrocytes and prevent their endothelial adhesion and target them for reticuloendothelial elimination. Band 3 is also displayed on the erythrocytes of individuals with falciparum malaria and the vaso-occlusive pathology in these patients is prevented in individuals with sickle trait. The hypothesis is that prematurely denatured sickle hemoglobin results in an up regulation of natural antibodies which control erythrocyte adhesion in both malaria and sickle cell disease.

Adsorption behavior of Fe atoms on a naphthalocyanine monolayer on Ag(111) surface

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

Yan, Ling -Hao; Wu, Rong -Ting; Bao, De -Liang

2015-05-29

Adsorption behavior of Fe atoms on a metal-free naphthalocyanine (H 2Nc) monolayer on Ag(111) surface at room temperature has been investigated using scanning tunneling microscopy combined with density functional theory (DFT) based calculations. We found that the Fe atoms adsorbed at the centers of H 2Nc molecules and formed Fe-H 2Nc complexes at low coverage. DFT calculations show that the configuration of Fe at the center of a molecule is the most stable site, in good agreement with the experimental observations. After an Fe-H 2Nc complex monolayer was formed, the extra Fe atoms self-assembled to Fe clusters of uniform sizemore » and adsorbed dispersively at the interstitial positions of Fe-H 2Nc complex monolayer. Furthermore, the H 2Nc monolayer grown on Ag(111) could be a good template to grow dispersed magnetic metal atoms and clusters at room temperature for further investigation of their magnetism-related properties.« less

Polymerization in the gas phase, in clusters, and on nanoparticle surfaces.

PubMed

El-Shall, M Samy

2008-07-01

Gas phase and cluster experiments provide unique opportunities to quantitatively study the effects of initiators, solvents, chain transfer agents, and inhibitors on the mechanisms of polymerization. Furthermore, a number of important phenomena, unique structures, and novel properties may exist during gas-phase and cluster polymerization. In this regime, the structure of the growing polymer may change dramatically and the rate coefficient may vary significantly upon the addition of a single molecule of the monomer. These changes would be reflected in the properties of the oligomers deposited from the gas phase. At low pressures, cationic and radical cationic polymerizations may proceed in the gas phase through elimination reactions. In the same systems at high pressure, however, the ionic intermediates may be stabilized, and addition without elimination may occur. In isolated van der Waals clusters of monomer molecules, sequential polymerization with several condensation steps can occur on a time scale of a few microseconds following the ionization of the gas-phase cluster. The cluster reactions, which bridge gas-phase and condensed-phase chemistry, allow examination of the effects of controlled states of aggregation. This Account describes several examples of gas-phase and cluster polymerization studies where the most significant results can be summarized as follows: (1) The carbocation polymerization of isobutene shows slower rates with increasing polymerization steps resulting from entropy barriers, which could explain the need for low temperatures for the efficient propagation of high molecular weight polymers. (2) Radical cation polymerization of propene can be initiated by partial charge transfer from an ionized aromatic molecule such as benzene coupled with covalent condensation of the associated propene molecules. This novel mechanism leads exclusively to the formation of propene oligomer ions and avoids other competitive products. (3) Structural information on the oligomers formed by gas-phase polymerization can be obtained using the mass-selected ion mobility technique where the measured collision cross-sections of the selected oligomer ions and collision-induced dissociation can provide fairly accurate structural identifications. The identification of the structures of the dimers and trimers formed in the gas-phase thermal polymerization of styrene confirms that the polymerization proceeds according to the Mayo mechanism. Similarly, the ion mobility technique has been utilized to confirm the formation of benzene cations by intracluster polymerization following the ionization of acetylene clusters. Finally, it has been shown that polymerization of styrene vapor on the surface of activated nanoparticles can lead to the incorporation of a variety of metal and metal oxide nanoparticles within polystyrene films. The ability to probe the reactivity and structure of the small growing oligomers in the gas phase can provide fundamental insight into mechanisms of polymerization that are difficult to obtain from condensed-phase studies. These experiments are also important for understanding the growth mechanisms of complex organics in flames, combustion processes, interstellar clouds, and solar nebula where gas-phase reactions, cluster polymerization, and surface catalysis on dust nanoparticles represent the major synthetic pathways. This research can lead to the discovery of novel initiation mechanisms and reaction pathways with applications in the synthesis of oligomers and nanocomposites with unique and improved properties.

Organization of Amphiphilic Molecular Disks with Branched Hydrophilic Tails and Hexa-peri-hexabenzocoronene Core

NASA Astrophysics Data System (ADS)

Lee, Myongsoo; Kim, Jung-Woo; Yoo, Yong-Sik; Peleshanko, Sergey; Larson, Kirsten; Vaknin, David; Markutsya, Sergei; Tsukruk, Vladimir V.

2002-03-01

Amphiphilic branched discotics consisting of the aromatic core and oligoethers as the branched peripheral chains have been characterized in bulk and monolayer states. The discotics based on di-branched oligoether side chains have been observed to self-organize into an ordered hexagonal columnar structure within liquid crystalline (LC) phases. The tetrabranched molecule showed only an isotropic liquid. The LC molecules with di-branched tails have been observed to form stable monolayers on the water surface in contrast to the tetra-branched tails. We suggest a crab-like molecular conformation and cluster-segregated monolayers with six-fold symmetry of face-on packing on a solid surface.

A Low Temperature, Ultrahigh Vacuum, Microwave-Frequency-Compatible Scanning Tunneling Microscope

DTIC Science & Technology

1994-05-01

vibrationally decoupled from the chamber using a Subadmed oo -3.- 21 April 1994 Reviw of Sdent* k Immownu Low Topasom UHV ACS7M Stranick et al...molecules, two isolated clusters of benzene molecules on the upper terrace, and several vacancy defects in the Cu(111) surface on the lower terrace...fine and is easily removed and replaced. 11. National Electrostatics Corporation, Middleton, WI. 12. K . Besocke, Surf. Sci. 181, 145 (1987); J. Frohn, J

Cluster self-organization of nanotubes in a nematic phase: The percolation behavior and appearance of optical singularities

NASA Astrophysics Data System (ADS)

Ponevchinsky, V. V.; Goncharuk, A. I.; Vasil'Ev, V. I.; Lebovka, N. I.; Soskin, M. S.

2010-03-01

The structural features, as well as the optical and electrophysical properties of a 5CB nematic liquid crystal with additions of multilayer carbon nanotubes, have been investigated in the concentration range C = 0.0025-0.1 wt %. The self-aggregation of nanotubes into clusters with a fractal structure occurs in the liquid crystal. At 0.025 wt %, the clusters are merged, initiating the percolation transition of the composite to a state with a high electric conductivity. The strong interaction of 5CB molecules with the surface of nanotube clusters is responsible for the formation of micron surface liquid crystal layers with an irregular field of elastic stresses and a complex structure of birefringence. They are easily observed in a polarization microscope and visualize directly invisible submicron nanotube aggregates. Their transverse size increases when an electric field is applied to the liquid crystal cell. Two mechanisms of the generation of optical singularities in the passing laser beam have been revealed. Optical vortices appear in the speckle fields of laser radiation scattered at the indented boundaries of the nanotube clusters, whereas the birefringence of the beam in surface liquid-crystal layers is accompanied by the appearance of polarization C points.

LASER APPLICATIONS AND OTHER TOPICS IN QUANTUM ELECTRONICS: Efficiency of passage of highly vibrationally excited CF3I molecules in a beam through a cooled converging hollow truncated cone

NASA Astrophysics Data System (ADS)

Makarov, Grigorii N.; Petin, A. N.

2006-09-01

The passage of CF3I molecules excited by high-intensity IR laser radiation to high vibrational states (with energy Ev >= 0.3-1.5 eV) and unexcited molecules in a pulsed beam through a converging truncated hollow metal cone cooled to Ts approx 80-85 K and mounted at an angle to the beam axis is studied. It is found that the excited molecules pass much more readily through the cone than the unexcited (vibrationally cold) molecules. This opens the possibility for studying the processes of energy transfer and redistribution over a cold surface covered by molecular (cluster) layers, and for separating excited and unexcited molecules in a beam.

Calculation of composition distribution of ultrafine ion-H2O-H2SO4 clusters using a modified binary ion nucleation theory

NASA Technical Reports Server (NTRS)

Singh, J. J.; Smith, A. S.; Chan, L. Y.; Yue, G. K.

1982-01-01

Thomson's ion nucleation theory was modified to include the effects of curvature dependence of the microscopic surface tension of field dependent, nonlinear, dielectric properties of the liquid; and of sulfuric acid hydrate formation in binary mixtures of water and sulfuric acid vapors. The modified theory leads to a broadening of the ion cluster spectrum, and shifts it towards larger numbers of H2O and H2SO4 molecules. Whether there is more shifting towards larger numbers of H2O or H2SO4 molecules depends on the relative humidity and relative acidity of the mixture. Usually, a broadening of the spectrum is accompanied by a lowering of the mean cluster intensity. For fixed values of relative humidity and relative acidity, a similar broadening pattern is observed when the temperature is lowered. These features of the modified theory illustrate that a trace of sulfuric acid can facilitate the formation of ultrafine, stable, prenucleation ion clusters as well as the growth of the prenucleation ion clusters towards the critical saddle point conditions, even with low values of relative humidity and relative acidity.

DFT study of CO2 and H2O co-adsorption on carbon models of coal surface.

PubMed

Gao, Zhengyang; Ding, Yi

2017-06-01

The moisture content of coal affects the adsorption capacity of CO 2 on the coal surface. Since the hydrogen bonds are formed between H 2 O and oxygen functional group, the H 2 O cluster more easily adsorbs on the coal micropore than CO 2 molecule. The coal micropores are occupied by H 2 O molecules that cannot provide extra space for CO 2 adsorption, which may leads to the reduction of CO 2 adsorption capacity. However, without considering factors of micropore and oxygen functional groups, the co-adsorption mechanisms of CO 2 and adsorbed H 2 O molecule are not clear. Density functional theory (DFT) calculations were performed to elucidate the effect of adsorbed H 2 O to CO 2 adsorption. This study reports some typical coal-H 2 O···CO 2 complexes, along with a detailed analysis of the geometry, energy, electrostatic potential (ESP), atoms in molecules (AIM), reduced density gradient (RDG), and energy decomposition analysis (EDA). The results show that H 2 O molecule can more stably adsorb on the aromatic ring surface than CO 2 molecule, and the absolute values of local ESP maximum and minimum of H 2 O cluster are greater than CO 2 . AIM analysis shows a detailed interaction path and strength between atoms in CO 2 and H 2 O, and RDG analysis shows that the interactions among CO 2 , H 2 O, and coal model belong to weak van der Waals force. EDA indicates that electrostatic and long-range dispersion terms play a primary role in the co-adsorption of CO 2 and H 2 O. According to the DFT calculated results without considering micropore structure and functional group, it is shown that the adsorbed H 2 O can promote CO 2 adsorption on the coal surface. These results demonstrate that the micropore factor plays a dominant role in affecting CO 2 adsorption capacity, the attractive interaction of adsorbed H 2 O to CO 2 makes little contribution.

Synthesis and energetics of gold nanoclusters tailored by interfacial bonding structure

NASA Astrophysics Data System (ADS)

Tang, Zhenghua

In addition to the well known quantum confinement effects resulted from size and shape, interfacial bond structure is another factor, affecting the properties of the nanomaterial that is rarely studied. Inspired by the "Au-S-Au" staple motif discovered from the crystal structure of monothiol protected Au102 nanocluster (Science, 2007, 318, 430), dithiol molecules (e.g. 1, 2-dithiol, 1, 4-dithiol, etc.) with molecular structural constraint have been employed to create dithiolate protected clusters or mixed monothiolate and dithiolate protected clusters. The structure and properties of the Au clusters are expected to change due to two effects: The entropy gain of dithiol over monothiol protection and the constraint to the formation of the thiol bridging motif. DMPS (1, 2-dithiol molecule) stabilized clusters with characteristic absorption bands have been obtained, and characterized by multiple techniques. Monolayer reaction on gold core surface between the monothiol tiopronin and dithiol DMPS has been performed, and the mechanism has been probed. Mixed phenylethanethiolate and durene-dithiolate (1, 4-dithiol molecule) protected Au130 clusters with rich electrochemical features have been created, and the optical and electrochemical energetics have been successfully correlated based on core and core-ligand energy states. Furthermore, the impact of 1, 4-dithiolate-Au bonding on the near infrared luminescence has been studied. INDEX WORDS: Au MPCs, Staple motif, DMPS, Au DTCs, Au4, Tiopronin, Monolayer reaction, Durene-DT, Au MTCs, Au130, Optical energetic, Electrochemistry, Near infrared luminescence, 1, 4-Dithiolate-Au bonding.

Organization of Single Molecule Magnets on Surfaces

NASA Astrophysics Data System (ADS)

Sessoli, Roberta

2006-03-01

The field of magnetic molecular clusters showing slow relaxation of the magnetization has attracted a great interest for the spectacular quantum effects in the dynamics of the magnetization that range from resonant quantum tunneling to topological interferences. Recently these systems, known as Single Molecule Magnets (SMMs), have also been proposed as model systems for the investigation of flame propagation in flammable substances. A renewed interest in SMMs also comes from the possibility to exploit their rich and complex magnetic behavior in nano-spintronics. However, at the crystalline state these molecular materials are substantially insulating. They can however exhibit significant transport properties if the conduction occurs through one molecule connected to two metal electrodes, or through a tunneling mechanism when the SMM is grafted on a conducting surface, as occurs in scanning tunnel microscopy experiments. Molecular compounds can be organized on surfaces thanks to the self assembly technique that exploits the strong affinity of some groups for the surface, e.g. thiols for gold surfaces. However the deposition of large molecules mainly comprising relatively weak coordinative bonds is far from trivial. Several different approaches have started to be investigated. We will briefly review here the strategies developed in a collaboration between the Universities of Florence and Modena. Well isolated molecules on Au(111) surfaces have been obtained with sub-monolayer coverage and different spacers. Organization on a large scale of micrometric structures has been obtained thanks to micro-contact printing. The magnetic properties of the grafted molecules have been investigated through magneto-optical techniques and the results show a significant change in the magnetization dynamics whose origin is still object of investigations.

Exploring the effect of oxygen-containing functional groups on the water-holding capacity of lignite.

PubMed

Liu, Jie; Jiang, Xiangang; Cao, Yu; Zhang, Chen; Zhao, Guangyao; Zhao, Maoshuang; Feng, Li

2018-05-07

Graphene oxide with different degrees of oxidation was prepared and selected as a model compound of lignite to study quantitatively, using both experiment and theoretical calculation methods, the effect on water-holding capacity of oxygen-containing functional groups. The experimental results showed that graphite can be oxidized, and forms epoxy groups most easily, followed by hydroxyl and carboxyl groups. The prepared graphene oxide forms a membrane-state as a single layer structure, with an irregular surface. The water-holding capacity of lignite increased with the content of oxygen-containing functional groups. The influence on the configuration of water molecule clusters and binding energy of water molecules of different oxygen-containing functional groups was calculated by density functional theory. The calculation results indicated that the configuration of water molecule clusters was totally changed by oxygen-containing functional groups. The order of binding energy produced by oxygen-containing functional groups and water molecules was as follows: carboxyl > edge phenol hydroxyl >epoxy group. Finally, it can be concluded that the potential to form more hydrogen bonds is the key factor influencing the interaction energy between model compounds and water molecules.

Ion-Ice Astrochemistry: Barrierless Low-Energy Deposition Pathways to HCOOH, CH3OH, and CO2 on Icy Grain Mantles from Precursor Cations

NASA Technical Reports Server (NTRS)

Woon, David E.

2011-01-01

A new family of very favorable reaction pathways is explored involving the deposition of ions on icy grain mantles with very low energies. Quantum chemical cluster calculations at the MP2/6-31+G** level in 4H2O clusters and at the B3LYP/6-31+G** level in 17H2O clusters indicate that HCO+ and CH3 + are able to react spontaneously with one of the water molecules in the cluster to form protonated formic acid (HCOOH2 +) and protonated methanol (CH3OH2 +), respectively. It is furthermore found that these initial adducts spontaneously transfer their excess protons to the cluster to form neutral formic acid and methanol, plus solvated hydronium, H3O+. In the final case, if a CO molecule is bound to the surface of the cluster, OH+ may react with it to form protonated carbon dioxide (HCO2 +), which then loses its proton to yield CO2 and H3O+. In the present model, all of these processes were found to occur with no barriers. Discussion includes the analogous gas phase processes, which have been considered in previous studies, as well as the competitive abstraction pathway for HCO(+) + H2O.

Nature of water and hydrogen reactions on transition metal surfaces studied by scanning tunneling microscopy

NASA Astrophysics Data System (ADS)

Tatarkhanov, Mouslim Magomedovich

Scanning Tunneling Microscopy (STM) has already been established as a tool for the investigation of simple reaction mechanisms. In this work I present results of two parallel studies using STM: first, hydrogen on Ru(0001) surface and second, water on Ru(0001) and Pd(111). In both studies initial stages of adsorption up to saturation monolayer coverage were investigated by variable temperature scanning tunneling microscopy (VT STM). The first step of the hydrogen adsorption study was the identification and characterization of the various coverage structures on clean Ru(0001). Hydrogen was found to adsorb dissociatively forming ( 3x3 )R30°, 3 domains of (2x1), (2x2)-3H and (1x1) for increasing coverages of theta=0.3 ML, 0.5 ML, 0.75 ML and 0.1 ML respectively. Some of these structures were observed to coexist at intermediate coverage values. In addition effects of impurities such as oxygen and carbon on hydrogen adsorption has been discussed. Next, near saturation coverage the interesting mechanism of how H 2 dissociates and binds to the surface of Ru(0001) has been observed. We found that the H2 dissociation takes place only on Ru sites where the metal atom is not bound to any H atom. Such active sites are formed when at least 3 H-vacancies aggregate by thermal diffusion. Sites formed by single H-vacancies (i.e. unoccupied Ru sites) or pairs of adjoining vacancies were found to be unreactive toward H2. H-vacancies were observed as single entities diffusing on the surface at 50 K and able to form transient triangular shaped aggregations where H2 molecules dissociated. It was found that the diffusion and aggregation of the H-vacancies is essential in creation of active sites where dissociative adsorption of hydrogen occurs. The first step of water studies was the initial stages of growth of water on the hexagonal surfaces of Pd(111) and Ru(0001) in the temperature range between 40 K and 130 K. In addition, DFT calculations and STM image simulations were used to validate the models. Below 130 K water dissociation does not occur at any appreciable rate and only molecular films are formed. At these temperatures the kinetics of water growth leads to structures where the molecules bind to the metal substrate through the O-lone pair while making 3 H-bonds with neighboring molecules and form clusters of hexagonal units with a honeycomb structure. This bonding geometry imposes limitations to the size of the clusters, with unsaturated H-bonds confined to the cluster periphery. It is found that growth proceeds by attachement of water molecules to the edge of the clusters by H-bonds. These molecules bind only weakly to the metal substrate and can hop around the edges. Comparison of DFT and STM image calculations with experiments shows that on Pd the edge-attached molecules form two different structures, a metastable one where the molecule is elevated by 2.7 A with respect to the cluster molecules, and another where they are elevated by only 0.4 A. On Ru only the less elevated (0.4 A higher) edge-attached molecules are observed. In next final step, water structures on Ru(0001) were studied at temperatures above 140K. STM findings were backed by x-ray absorption spectroscopy. Additional DFT calculations and STM simulations provided validation of proposed models. It was found that while undissociated water layers are metastable below 140 K, heating above this temperature produces drastic transformations whereby a fraction of the water molecules partially dissociate and form mixed H 2O-OH structures. XPS and XAS revealed the presence of hydroxyl groups with their O-H bond essentiallymostly parallel to the surface. STM images show that the mixed H2O-OH structures consist of long narrow stripes aligned with the three crystallographic directions perpendicular to the close-packed atomic rows of the Ru(0001) substrate. The internal structure of the stripes is a honeycomb network of H-bonded water and hydroxyl species. We found that the metastable low temperature molecular phase can also be converted to a mixed H2O-OH phase through excitation by the tunneling electrons when their energy is 0.5 eV or higher above the Fermi level. Structural models based on the STM images were used for Density Functional Theory optimizations of the stripes geometry. The optimized geometry was then utilized to calculate STM images for comparison with the experiment.

CO2 adsorption on gas-phase Cu4-xPtx (x = 0-4) clusters: a DFT study.

PubMed

Gálvez-González, Luis E; Juárez-Sánchez, J Octavio; Pacheco-Contreras, Rafael; Garzón, Ignacio L; Paz-Borbón, Lauro Oliver; Posada-Amarillas, Alvaro

2018-06-13

Transition and noble metal clusters have proven to be critical novel materials, potentially offering major advantages over conventional catalysts in a range of value-added catalytic processess such as carbon dioxide transformation to methanol. In this work, a systematic computational study of CO2 adsorption on gas-phase Cu4-xPtx (x = 0-4) clusters is performed. An exhaustive potential energy surface exploration is initially performed using our recent density functional theory basin-hopping global optimization implementation. Ground-state and low-lying energy isomers are identified for Cu4-xPtx clusters. Secondly, a CO2 molecule adsorption process is analyzed on the ground-state Cu4-xPtx configurations, as a function of cluster composition. Our results show that the gas-phase linear CO2 molecule is deformed upon adsorption, with its bend angle varying from about 132° to 139°. Cu4-xPtx cluster geometries remain unchanged after CO2 adsorption, with the exception of Cu3Pt1 and Pt4 clusters. For these particular cases, a structural conversion between the ground-state geometry and the corresponding first isomer configurations is found to be assisted by the CO2 adsorption. For all clusters, the energy barriers between the ground-state and first isomer structures are explored. Our calculated CO2 adsorption energies are found to be larger for Pt-rich clusters, exhibiting a volcano-type plot. The overall effect of a hybrid functional including dispersion forces is also discussed.

Organic Molecules On the Surfaces of Iapetus and Phoebe

NASA Technical Reports Server (NTRS)

Pendleton, Yvonne J.; Dalle Ore, Cristina M.; Clark, Roger N.; Cruikshank, Dale P.

2017-01-01

Absorption bands of both aliphatic and aromatic organic molecules are found in the reflectance spectra of Saturn satellites Iapetus, Phoebe, and Hyperion obtained with the Cassini Visible-Infrared Mapping Spectrometer (VIMS). The VIMS data do not fully resolve the individual bands of C-H functional groups specific to particular molecules, but instead show absorption envelopes representing blended clusters of the bands of aromatic (approximately 3.28 microns) and aliphatic (approximately 3.4 microns) hydrocarbons known in spectra of interstellar dust. In Cruikshank et al. (2014), we matched components of the unresolved hydrocarbon band envelopes with clusters of bands of a range of functional groups in specific types of organic compounds (e.g., normal and N-substituted polycyclic aromatic hydrocarbons, olefins, cycloalkanes, and molecules with lone-pair interactions of N and O with CH3+). In the work reported here, we revisit the spectra of Iapetus and Phoebe using VIMS data processed with improved radiometric and wavelength calibration (denoted RC19). The band envelopes of both aromatic and aliphatic hydrocarbons are now more clearly defined, corroborating the provisional assignment of specific classes of molecules in Cruikshank et al. 2014, but permitting a more reliable quantitative assessment of the relative contributions of those classes, and a revision to the earlier estimate of the ratio of the abundances of aromatic to aliphatic molecules.

Isomerization of one molecule observed through tip enhanced Raman spectroscopy

NASA Astrophysics Data System (ADS)

Zhang, Yanxing; Lee, Joonhee; Apkarian, Vartkess A.; Wu, Ruqian; Ruqian Wu, Yanxing Zhang Team; Joonhee Lee, Vartkess A. Apkarian Team

While exploring photoisomerization of azobenzyl thiols (ABT) adsorbed on Au(111), through joint scanning tunneling microscopy (STM) and tip-enhanced Raman scattering (TERS) studies, the reversible photoisomerization of one molecule is captured in TERS trajectories. The apparently heterogeneously photo-catalyzed reaction is assigned to cis-trans isomerization of an outlier, which is chemisorbed on the silver tip of the STM. In order to clarify the role of the silver tip of the STM, we perform systematic density functional theory (DFT) calculations. The results show that compared with the case on the flat Ag(111) surface, the energy difference between trans and cis states of ABT decrease as we add one silver atom or a tetrahedron silver cluster on Ag(111) surface which mimic the geometry of a silver tip. In particular, the trans stretches away from the surface on the tetrahedral silver cluster, and the energy difference between trans and cis decreases to 0.27 eV, from ~1 eV for ABT on the flat Ag(111) surface. This significantly increases the possibility of cis-trans isomerization, as observed in our experiments. Work was supported by the National Science Foundation Center for Chemical Innovation on Chemistry at the Space-Time Limit (CaSTL) under Grant No. CHE-1414466.

Theory of liquid crystal orientation under action of light wave field and aligning surfaces

NASA Astrophysics Data System (ADS)

Dadivanyan, A. K.; Chausov, D. N.; Belyaev, V. V.; Barabanova, N. N.; Chausova, O. V.; Kuleshova, Yu D.

2018-03-01

Theoretical models developed in the MRSU group under leadership of Professor Artem Dadivanyan in area of the LC orientation and photo-induced effects are presented. Angular distribution functions of the dye and liquid crystal molecules under action of intensive light beam have been derived. The number of molecules in cluster is estimated. A model of dimers formation in the photoalignment dye is suggested that explains influence of the dye molecular structure on both polar and azimuthal anchoring energy.

Towards DNA-Based Programmable Matter

DTIC Science & Technology

2012-02-28

optics. Nature 2003, 424, 824–830. (2) Xu, H. X.; Bjerneld, E. J.; Kall , M.; Borjesson, L. Spectroscopy of single hemoglobin molecules by surface...Brenner, M. P.; Manoharan, V. N. The Free-energy Landscape of Clusters of Attractive Hard Spheres. Science 2010, 327, 560–563. (35) Xu, H. X.; Kall , M

CD Nomenclature 2015: Human Leukocyte Differentiation Antigen Workshops as a Driving Force in Immunology.

PubMed

Engel, Pablo; Boumsell, Laurence; Balderas, Robert; Bensussan, Armand; Gattei, Valter; Horejsi, Vaclav; Jin, Bo-Quan; Malavasi, Fabio; Mortari, Frank; Schwartz-Albiez, Reinhard; Stockinger, Hannes; van Zelm, Menno C; Zola, Heddy; Clark, Georgina

2015-11-15

CD (cluster of differentiation) Ags are cell surface molecules expressed on leukocytes and other cells relevant for the immune system. CD nomenclature has been universally adopted by the scientific community and is officially approved by the International Union of Immunological Societies and sanctioned by the World Health Organization. It provides a unified designation system for mAbs, as well as for the cell surface molecules that they recognize. This nomenclature was established by the Human Leukocyte Differentiation Antigens Workshops. In addition to defining the CD nomenclature, these workshops have been instrumental in identifying and determining the expression and function of cell surface molecules. Over the past 30 y, the data generated by the 10 Human Leukocyte Differentiation Antigens Workshops have led to the characterization and formal designation of more than 400 molecules. CD molecules are commonly used as cell markers, allowing the identification and isolation of leukocyte populations, subsets, and differentiation stages. mAbs against these molecules have proven to be essential for biomedical research and diagnosis, as well as in biotechnology. More recently, they have been recognized as invaluable tools for the treatment of several malignancies and autoimmune diseases. In this article, we describe how the CD nomenclature was established, present the official updated list of CD molecules, and provide a rationale for their usefulness in the 21st century. Copyright © 2015 by The American Association of Immunologists, Inc.

Sequential desorption energy of hydrogen from nickel clusters

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

Deepika,; Kumar, Rakesh, E-mail: rakesh@iitrpr.ac.in; R, Kamal Raj.

2015-06-24

We report reversible Hydrogen adsorption on Nickel clusters, which act as a catalyst for solid state storage of Hydrogen on a substrate. First-principles technique is employed to investigate the maximum number of chemically adsorbed Hydrogen molecules on Nickel cluster. We observe a maximum of four Hydrogen molecules adsorbed per Nickel atom, but the average Hydrogen molecules adsorbed per Nickel atom decrease with cluster size. The dissociative chemisorption energy per Hydrogen molecule and sequential desorption energy per Hydrogen atom on Nickel cluster is found to decrease with number of adsorbed Hydrogen molecules, which on optimization may help in economical storage andmore » regeneration of Hydrogen as a clean energy carrier.« less

Invariant Chain Complexes and Clusters as Platforms for MIF Signaling

PubMed Central

Lindner, Robert

2017-01-01

Invariant chain (Ii/CD74) has been identified as a surface receptor for migration inhibitory factor (MIF). Most cells that express Ii also synthesize major histocompatibility complex class II (MHC II) molecules, which depend on Ii as a chaperone and a targeting factor. The assembly of nonameric complexes consisting of one Ii trimer and three MHC II molecules (each of which is a heterodimer) has been regarded as a prerequisite for efficient delivery to the cell surface. Due to rapid endocytosis, however, only low levels of Ii-MHC II complexes are displayed on the cell surface of professional antigen presenting cells and very little free Ii trimers. The association of Ii and MHC II has been reported to block the interaction with MIF, thus questioning the role of surface Ii as a receptor for MIF on MHC II-expressing cells. Recent work offers a potential solution to this conundrum: Many Ii-complexes at the cell surface appear to be under-saturated with MHC II, leaving unoccupied Ii subunits as potential binding sites for MIF. Some of this work also sheds light on novel aspects of signal transduction by Ii-bound MIF in B-lymphocytes: membrane raft association of Ii-MHC II complexes enables MIF to target Ii-MHC II to antigen-clustered B-cell-receptors (BCR) and to foster BCR-driven signaling and intracellular trafficking. PMID:28208600

In Situ Observations of UV-Induced Restructuring of Self-Assembled Porphyrin Monolayer on Liquid/Au(111) Interface at Molecular Level.

PubMed

Kim, Yongman; Doh, Won Hui; Kim, Jeongjin; Park, Jeong Young

2018-05-29

Porphyrin-derived molecules have received much attention for use in solar energy conversion devices, such as artificial leaves and dye-sensitized solar cells. Because of their technological importance, a molecular-level understanding of the mechanism for supramolecular structure formation in a liquid, as well as their stability under ultraviolet (UV) irradiation, is important. Here, we observed the self-assembled structure of free-base, copper(II), and nickel(II) octaethylporphyrin formed on Au(111) in a dodecane solution using scanning tunneling microscopy (STM). As evident in the STM images, the self-assembled monolayers (SAMs) of these three porphyrins on the Au(111) surface showed hexagonal close-packed structures when in dodecane solution. Under UV irradiation (λ = 365 nm), the porphyrin molecules in the SAM or the dodecane solution move extensively and form new porphyrin clusters on the Au sites that have a high degree of freedom. Consequently, the Au(111) surface was covered with disordered porphyrin clusters. However, we found that the porphyrin molecules decomposed under UV irradiation at 254 nm. Molecular-scale observation of the morphological evolution of the porphyrin SAM under UV irradiation can provide a fundamental understanding of the degradation processes of porphyrin-based energy conversion devices.

Synthesis of borophenes: Anisotropic, two-dimensional boron polymorphs

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

Mannix, A. J.; Zhou, X. -F.; Kiraly, B.

At the atomic-cluster scale, pure boron is markedly similar to carbon, forming simple planar molecules and cage-like fullerenes. Theoretical studies predict that two-dimensional (2D) boron sheets will adopt an atomic configuration similar to that of boron atomic clusters. We synthesized atomically thin, crystalline 2D boron sheets (i.e., borophene) on silver surfaces under ultrahigh-vacuum conditions. Atomic-scale characterization, supported by theoretical calculations, revealed structures reminiscent of fused boron clusters with multiple scales of anisotropic, out-of-plane buckling. Unlike bulk boron allotropes, borophene shows metallic characteristics that are consistent with predictions of a highly anisotropic, 2D metal.

Transcriptional analysis of exopolysaccharides biosynthesis gene clusters in Lactobacillus plantarum.

PubMed

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.

Thermodynamic properties of water solvating biomolecular surfaces

NASA Astrophysics Data System (ADS)

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.

Electrical and galvanomagnetic properties of nanoporous carbon samples impregnated with bromine

NASA Astrophysics Data System (ADS)

Danishevskii, A. M.; Popov, V. V.; Kyutt, R. N.; Gordeev, S. K.

2013-07-01

Nanoporous carbon samples with a large specific surface area can be filled with heavier elements or their compounds, which makes it possible to investigate the interaction of their electronic subsystems with carbon. One of the elements convenient for filling pores of carbon materials is bromine. Impregnation of nanoporous carbon samples with bromine causes the occurrence of the processes of micropore filling, monolayer adsorption, and intercalation. It has been found that samples impregnated with bromine substantially change their electrical and galvanomagnetic properties, and these changes depend on the structure of the samples. It has been shown that, if in the skeleton of a porous carbon sample there is a fraction of graphite clusters, the impregnation of the sample with bromine increases the concentration of charged carriers (holes). But when the sample has a quasi-amorphous structure, the injection of bromine into the sample leads to the appearance of a certain concentration of electrons in addition to charged mobile holes of the initial sample; i.e., the electrical conductivity becomes bipolar. In the former case, bromine molecules intercalate graphite clusters and, since bromine is an acceptor during intercalation of graphite, the hole concentration in the carbon skeleton network increases. In the latter case, bromine molecules can only be adsorbed on pore walls. As a result, the adsorption interaction between the electron shells of bromine molecules and the carbon surface leads to the formation of a donor layer near the surface and to the generation of electrons in the carbon skeleton network.

Theoretical study on mechanisms of structural rearrangement and ionic dissociation in the HCl(H 2O) 4 cluster with path-integral molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Sugawara, Shuichi; Yoshikawa, Takehiro; Takayanagi, Toshiyuki; Tachikawa, Masanori

2011-01-01

The structural rearrangement process for the HCl(H2O)4 cluster has been studied by path-integral molecular dynamics simulations, where 'on-the-fly' calculation of the potential energy surface is done with the PM3-MAIS semiempirical level. The mechanisms of the rearrangement were analyzed using appropriate collective coordinates as well as detailed potential energy diagrams derived from low-lying stationary points. It was found that the vibrational entropy mainly determines the stability of the cluster structure especially at high temperatures. We have also found that the acidity of HCl in the cluster correlates with the coordination number of chlorine with respect water molecules.

Isomer-Specific IR Spectroscopy of BENZENE-(WATER)N Clusters with N=1-8: New Insights from the Water Bend Fundamentals and Isotopically Substituted Clusters

NASA Astrophysics Data System (ADS)

Kusaka, Ryoji; Walsh, Patrick S.; Zwier, Timothy S.

2014-06-01

This talk will focus on the isomer-specific IR spectra of benzene-(water)n (BWn) clusters with n = 1-8, returning to a topic studied by our group some 20 years ago, but now with higher resolution (OH stretch region), with inclusion of data from isotopically substituted clusters, and with extension into the HOH bending mode region. Spectra are recorded using resonant ion-dip infrared spectroscopy, an IR-UV double resonance method. Isomer-specific IR spectra in the regions of OH, OD stretches and HOH, HOD bend of benzene-H_2O, -D_2O, -HOD, -(H_2O)_2, -(D_2O)_2, -HOD-DOD were recorded in order to investigate in greater detail the intermolecular potential energy surface between water and benzene. These spectra show strong combination bands in addition to the OH/OD stretch fundamentals arising from large-amplitude "tumbling" and tunneling along internal rotation and torsion coordinates of water(s) on the surface of benzene. Interestingly, the number of extra bands and spectral patterns change dramatically depending on cluster size, the kind of deuterated isomer, and the spectral region probed. In larger clusters with n=3-8, the water HOH bending region is explored for the first time. The prominent bending mode transitions in BW1-8 are spread over a relatively small range (1610-1660 wn), and shift with cluster size in a way that reflects the known structural changes that accompany the increase in size. By comparison of experiment with calculation, it is possible to assign the experimentally observed 1614 wn transition of BW1 and 1615 wn of BW2 bands to the π-bound water molecule. The 1620-1660 wn bands of BW3-8 are due to water molecules that can be categorized as single-acceptor, single-donor (AD) hydrogen-bonded waters. In the case of single-acceptor, double-donor (ADD) water molecules, which are expected to be seen from BW6,a they show higher-frequency bending vibrations and weaker IR intensity, which would correspond to very weakly observed bands in 1660-1750 wn for BW6-8. R. N. Pribble and T. S. Zwier, Science, 1994, 265, 75-79.

Multiscale benchmarking of drug delivery vectors.

PubMed

Summers, Huw D; Ware, Matthew J; Majithia, Ravish; Meissner, Kenith E; Godin, Biana; Rees, Paul

2016-10-01

Cross-system comparisons of drug delivery vectors are essential to ensure optimal design. An in-vitro experimental protocol is presented that separates the role of the delivery vector from that of its cargo in determining the cell response, thus allowing quantitative comparison of different systems. The technique is validated through benchmarking of the dose-response of human fibroblast cells exposed to the cationic molecule, polyethylene imine (PEI); delivered as a free molecule and as a cargo on the surface of CdSe nanoparticles and Silica microparticles. The exposure metrics are converted to a delivered dose with the transport properties of the different scale systems characterized by a delivery time, τ. The benchmarking highlights an agglomeration of the free PEI molecules into micron sized clusters and identifies the metric determining cell death as the total number of PEI molecules presented to cells, determined by the delivery vector dose and the surface density of the cargo. Copyright © 2016 Elsevier Inc. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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.

Modeling collective behavior of molecules in nanoscale direct deposition processes

NASA Astrophysics Data System (ADS)

Lee, Nam-Kyung; Hong, Seunghun

2006-03-01

We present a theoretical model describing the collective behavior of molecules in nanoscale direct deposition processes such as dip-pen nanolithography. We show that strong intermolecular interactions combined with nonuniform substrate-molecule interactions can produce various shapes of molecular patterns including fractal-like structures. Computer simulations reveal circular and starlike patterns at low and intermediate densities of preferentially attractive surface sites, respectively. At large density of such surface sites, the molecules form a two-dimensional invasion percolation cluster. Previous experimental results showing anisotropic patterns of various chemical and biological molecules correspond to the starlike regime [P. Manandhar et al., Phys. Rev. Lett. 90, 115505 (2003); J.-H. Lim and C. A. Mirkin, Adv. Mater. (Weinheim, Ger.) 14, 1474 (2002); D. L. Wilson et al., Proc. Natl. Acad. Sci. U.S.A. 98, 13660 (2001); M. Su et al., Appl. Phys. Lett. 84, 4200 (2004); R. McKendry et al., Nano Lett. 2, 713 (2002); H. Zhou et al., Appl. Surf. Sci. 236, 18 (2004); G. Agarwal et al., J. Am. Chem. Soc. 125, 580 (2003)].

Structural and dynamical characterization of water on the Au (100) and graphene surfaces: A molecular dynamics simulation approach

NASA Astrophysics Data System (ADS)

Foroutan, Masumeh; Darvishi, Mehdi; Fatemi, S. Mahmood

2017-09-01

The positioning, adsorption, and movement of water on substrates is dependent upon the chemical nature and arrangement of the atoms of the surface. Therefore the behavior of water molecules on a substrate is a reflection of properties of the surface. Based on this premise, graphene and gold substrates were chosen to study this subject from a molecular perspective. In this work, the structural and dynamical behaviors of a water nanodroplet on Au (100) and the graphene interfaces have been studied by molecular dynamics simulation. The results have shown how the structural and dynamical behaviors of water molecules at the interface reflect the characteristics of these surfaces. The results have demonstrated that residence time and hydrogen bonds' lifetime at the water-Au (100) interface are bigger than at the water-graphene interface. Energy contour map analysis indicates a more uniform surface energy on graphene than on the gold surface. The obtained results illustrate that water clusters on gold and graphene form tetramer and hexamer structures, respectively. Furthermore, the water molecules are more ordered on the gold surface than on graphene. The study of hydrogen bonds showed that the order, stability, and the number of hydrogen bonds is higher on the gold surface. The positioning pattern of water molecules is also similar to the arrangement of gold atoms while no regularity was observed on graphene. The study of dynamical behavior of water molecules revealed that the movement of water on gold is much less than on graphene which is in agreement with the strong water-gold interaction in comparison to the water-graphene interaction.

The Human Natural Killer Cell Immune Synapse

NASA Astrophysics Data System (ADS)

Davis, Daniel M.; Chiu, Isaac; Fassett, Marlys; Cohen, George B.; Mandelboim, Ofer; Strominger, Jack L.

1999-12-01

Inhibitory killer Ig-like receptors (KIR) at the surface of natural killer (NK) cells induced clustering of HLA-C at the contacting surface of target cells. In this manner, inhibitory immune synapses were formed as human NK cells surveyed target cells. At target/NK cell synapses, HLA-C/KIR distributed into rings around central patches of intercellular adhesion molecule-1/lymphocyte function-associated antigen-1, the opposite orientation to mature murine T cell-activating synapses. This organization of protein was stable for at least 20 min. Cells could support multiple synapses simultaneously, and clusters of HLA-C moved as NK cells crawled over target cells. Clustering required a divalent metal cation, explaining how metal chelators inhibit KIR function. Surprisingly, however, formation of inhibitory synapses was unaffected by ATP depletion and the cytoskeletal inhibitors, colchicine and cytochalsins B and D. Clearly, supramolecular organization within plasma membranes is critical for NK cell immunosurveillance.

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

NASA Astrophysics Data System (ADS)

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.

Proton dynamics and surface heterogeneity of silica gel with adsorbed benzene below one monolayer coverage

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

Peterson, E.M.; O'Reilly, D.E.; Tsangb), T.

1979-04-01

Proton and deuteron NMR relaxation times of C/sub 6/H/sub 6/, C/sub 6/D/sub 6/, and mixtures of these molecules have been measured on a superpure silica gel (SPSG) and a sample of a Matheson silica gel (MSG) both dehydrated at 600/sup 0/ C and rotational (intramolecular) and translational (intermolecular) correlation times have been computed from the relaxation time data at a statistical coverage theta=0.6. Three kinds of adsorption sites have been observed: (1) A sites, which are probably oxygen vacancies on the surface, (2) B sites which are assigned to paired hydroxyl groups on the surface, and finally (3) C sitesmore » which comprise 80% of the occupied surface and are primarily isolated hydroxyl groups. Rotational and translational motions are highly correlated for the A and B site molecules. The mean number of molecules clustered at the A and B sites are inferred from the intermolecular second moments associated with each of these sites. The surface density of the A sites is 1.1 x 10/sup 12/ cm/sup -2/ for SPSG and 3.1 x 10/sup 12/ cm/sup -2/ for MSG.« less

Interfacial Mechanisms of Water Vapor Sorption into Cellulose Nanofibril Films as Revealed by Quantitative Models.

PubMed

Hakalahti, Minna; Faustini, Marco; Boissière, Cédric; Kontturi, Eero; Tammelin, Tekla

2017-09-11

Humidity is an efficient instrument for facilitating changes in local architectures of two-dimensional surfaces assembled from nanoscaled biomaterials. Here, complementary surface-sensitive methods are used to collect explicit and precise experimental evidence on the water vapor sorption into (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO) oxidized cellulose nanofibril (CNF) thin film over the relative humidity (RH) range from 0 to 97%. Changes in thickness and mass of the film due to water vapor uptake are tracked using spectroscopic ellipsometry and quartz crystal microbalance with dissipation monitoring, respectively. Experimental data is evaluated by the quantitative Langmuir/Flory-Huggins/clustering model and the Brunauer-Emmett-Teller model. The isotherms coupled with the quantitative models unveil distinct regions of predominant sorption modes: specific sorption of water molecules below 10% RH, multilayer build-up between 10 to 75% RH, and clustering of water molecules above 75% RH. The study reveals the sorption mechanisms underlying the well-known water uptake behavior of TEMPO oxidized CNF directly at the gas-solid interface.

Stabilities of protonated water-ammonia clusters

NASA Astrophysics Data System (ADS)

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.

Physical, Spatial, and Molecular Aspects of Extracellular Matrix of In Vivo Niches and Artificial Scaffolds Relevant to Stem Cells Research

PubMed Central

Akhmanova, Maria; Osidak, Egor; Domogatsky, Sergey; Rodin, Sergey; Domogatskaya, Anna

2015-01-01

Extracellular matrix can influence stem cell choices, such as self-renewal, quiescence, migration, proliferation, phenotype maintenance, differentiation, or apoptosis. Three aspects of extracellular matrix were extensively studied during the last decade: physical properties, spatial presentation of adhesive epitopes, and molecular complexity. Over 15 different parameters have been shown to influence stem cell choices. Physical aspects include stiffness (or elasticity), viscoelasticity, pore size, porosity, amplitude and frequency of static and dynamic deformations applied to the matrix. Spatial aspects include scaffold dimensionality (2D or 3D) and thickness; cell polarity; area, shape, and microscale topography of cell adhesion surface; epitope concentration, epitope clustering characteristics (number of epitopes per cluster, spacing between epitopes within cluster, spacing between separate clusters, cluster patterns, and level of disorder in epitope arrangement), and nanotopography. Biochemical characteristics of natural extracellular matrix molecules regard diversity and structural complexity of matrix molecules, affinity and specificity of epitope interaction with cell receptors, role of non-affinity domains, complexity of supramolecular organization, and co-signaling by growth factors or matrix epitopes. Synergy between several matrix aspects enables stem cells to retain their function in vivo and may be a key to generation of long-term, robust, and effective in vitro stem cell culture systems. PMID:26351461

Interaction of different poisons with MgCl2/TiCl4 based Ziegler-Natta catalysts

NASA Astrophysics Data System (ADS)

Bahri-Laleh, Naeimeh

2016-08-01

Adsorption of different poison molecules on activated MgCl2 is investigated within DFT using a cluster model of the MgCl2 surface with (MgCl2)16 formula containing four 4-coordinated and eight 5-coordinated Mg atoms as (110) and (104) surfaces, respectively. Studied poison molecules are chosen as possible impurities in hydrocarbon solvents and monomer feeds and contain water, hydrogensulfide, carbondioxide, molecular oxygen and methanol. First, adsorption of 1-4 molecules of different poisons to the (104) and (110) lateral cuts of MgCl2, as well as their adsorption on [MgCl2]/TiCl2Et active center and AlEt3 cocatalyst is considered. Results reveal that poisons strongly stabilize both crystal surfaces, mostly Ti active center relative to the unpoisoned solid. Second, energy barrier (ETS) for ethylene insertion in the presence of different poisons located on the first and second Mg atom relative to the active Ti is calculated. While poison molecule located on the second Mg does not change ETS, coordination of it into the first Mg atom increases ETS by 0.9-1.2 kcal mol-1. In the last part of this manuscript, the stereoselective behavior of active Ti species, with and without poison molecules and external electron donor, is fully explored.

Heterogeneous catalysis with lasers

NASA Astrophysics Data System (ADS)

George, T. F.

1986-06-01

Theoretical techniques have been developed to describe a variety of laser-induced molecular rate processes occurring at solid surfaces which are involved in heterogeneous catalysis. Such processes include adsorption, migration, chemical reactions and desorption. The role of surface phonons in laser-selective processes and laser heating has been analyzed. The importance of electronic degrees of freedom has been considered for semiconductor and metal substrates, with special emphasis on the laser excitation of surface states. Surface-modified photochemistry has also been investigated, where the effect of a metal surface on the resonance fluorescence spectrum of a laser-driven atom/molecule has been assessed by means of surface-dressed optical Bloch equations. It is seen that the spectrum can be significantly different from the gas-phase case. Two related gas-surface collision processes have also been studied. First, the feasibility of the formation of the electron-hole pairs in a semiconductor by vibrationally excited molecules has been explored. Second, charge transfer in ion-surface collisions has been examined for both one-electron and two-electron transfer processes. Work has been initiated on microstructures and rough structures, including clusters and surface gratings.

What is the minimum number of water molecules required to dissolve a potassium chloride molecule?

PubMed

Sen, Anik; Ganguly, Bishwajit

2010-12-01

This work answers an unsolved question that consists of determining the least number of water molecules necessary to separate a potassium chloride molecule. The answer based on accurate quantum chemical calculations suggests that tetramers are the smallest clusters necessary to dissociate KCl molecules. The study was made with Møller-Plesset second-order perturbation theory modified with the cluster theory having single, double, and perturbative triple excitations. With this extensive study, the dissociation of KCl molecule in different water clusters was evaluated. The calculated results show that four water molecules stabilize a solvent separated K(+)/Cl(-) ion-pair in prismatic structure and with six water molecules further dissociation was observed. Attenuated total reflection infrared spectroscopy of KCl dissolved in water establishes that clusters are made of closely bound ions with a mean of five water molecules per ion-pair [K(+)(H(2)O)(5)Cl(-)]. (Max and Chapados, Appl Spectrosc 1999, 53, 1601; Max and Chapados, J Chem Phys 2001, 115, 2664.) The calculated results tend to support that five water molecules leads toward the formation of contact ion-pair. The structures, energies, and infrared spectra of KCl molecules in different water clusters are also discussed. © 2010 Wiley Periodicals, Inc.

Evolution of the properties of Al(n)N(n) clusters with size.

PubMed

Costales, Aurora; Blanco, M A; Francisco, E; Pandey, Ravindra; Martín Pendás, A

2005-12-29

A global optimization of stoichiometric (AlN)(n) clusters (n = 1-25, 30, 35, ..., 95, 100) has been performed using the basin-hopping (BH) method and describing the interactions with simple and yet realistic interatomic potentials. The results for the smaller isomers agree with those of previous electronic structure calculations, thus validating the present scheme. The lowest-energy isomers found can be classified in three different categories according to their structural motifs: (i) small clusters (n = 2-5), with planar ring structures and 2-fold coordination, (ii) medium clusters (n = 6-40), where a competition between stacked rings and globular-like empty cages exists, and (iii) large clusters (n > 40), large enough to mix different elements of the previous stage. All the atoms in small and medium-sized clusters are in the surface, while large clusters start to display interior atoms. Large clusters display a competition between tetrahedral and octahedral-like features: the former lead to a lower energy interior in the cluster, while the latter allow for surface terminations with a lower energy. All of the properties studied present different regimes according to the above classification. It is of particular interest that the local properties of the interior atoms do converge to the bulk limit. The isomers with n = 6 and 12 are specially stable with respect to the gain or loss of AlN molecules.

Adhesion of protein residues to substituted (111) diamond surfaces: an insight from density functional theory and classical molecular dynamics simulations.

PubMed

Borisenko, Konstantin B; Reavy, Helen J; Zhao, Qi; Abel, Eric W

2008-09-15

Protein-repellent diamond coatings have great potential value for surface coatings on implants and surgical instruments. The design of these coatings relies on a fundamental understanding of the intermolecular interactions involved in the adhesion of proteins to surfaces. To get insight into these interactions, adhesion energies of glycine to pure and Si and N-doped (111) diamond surfaces represented as clusters were calculated in the gas phase, using density functional theory (DFT) at the B3LYP/6-31G* level. The computed adhesion energies indicated that adhesion of glycine to diamond surface may be modified by introducing additional elements into the surface. The adhesion was also found to induce considerable change in the conformation of glycine when compared with the lowest-energy conformer of the free molecule. In the Si and N-substituted diamond clusters, notable changes in the structures involving the substituents atoms when compared with smaller parent molecules, such as 1-methyl-1-silaadamantane and 1-azaadamantane, were detected. Adhesion free energy differences were estimated for a series of representative peptides (hydrophobic Phe-Gly-Phe, amphiphilic Arg-Gly-Phe, and hydrophilic Arg-Gly-Arg) to a (111) diamond surface substituted with different amounts of N, Si, or F, using molecular dynamics simulations in an explicit water environment employing a Dreiding force field. The calculations were in agreement with the DFT results in that adsorption of the studied peptides to diamond surface is influenced by introducing additional elements to the surface. It has been shown that, in general, substitution will enhance electrostatic interactions between a surface and surrounding water, leading to a weaker adhesion of the studied peptides.

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

PubMed

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

2014-07-21

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.

Synthesis of borophenes: Anisotropic, two-dimensional boron polymorphs.

PubMed

Mannix, Andrew J; Zhou, Xiang-Feng; Kiraly, Brian; Wood, Joshua D; Alducin, Diego; Myers, Benjamin D; Liu, Xiaolong; Fisher, Brandon L; Santiago, Ulises; Guest, Jeffrey R; Yacaman, Miguel Jose; Ponce, Arturo; Oganov, Artem R; Hersam, Mark C; Guisinger, Nathan P

2015-12-18

At the atomic-cluster scale, pure boron is markedly similar to carbon, forming simple planar molecules and cage-like fullerenes. Theoretical studies predict that two-dimensional (2D) boron sheets will adopt an atomic configuration similar to that of boron atomic clusters. We synthesized atomically thin, crystalline 2D boron sheets (i.e., borophene) on silver surfaces under ultrahigh-vacuum conditions. Atomic-scale characterization, supported by theoretical calculations, revealed structures reminiscent of fused boron clusters with multiple scales of anisotropic, out-of-plane buckling. Unlike bulk boron allotropes, borophene shows metallic characteristics that are consistent with predictions of a highly anisotropic, 2D metal. Copyright © 2015, American Association for the Advancement of Science.

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

NASA Astrophysics Data System (ADS)

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.

Properties of Ammonium Ion–Water Clusters: Analyses of Structure Evolution, Noncovalent Interactions, and Temperature and Humidity Effects

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

Pei, Shi-Tu; Jiang, Shuai; Liu, Yi-Rong

2015-03-03

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 ofmore » 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.« less

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

PubMed

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.

Free energy barriers for escape of water molecules from protein hydration layer.

PubMed

Roy, Susmita; Bagchi, Biman

2012-03-08

Free energy barriers separating interfacial water molecules from the hydration layer at the surface of a protein to the bulk are obtained by using the umbrella sampling method of free energy calculation. We consider hydration layer of chicken villin head piece (HP-36) which has been studied extensively by molecular dynamics simulations. The free energy calculations reveal a strong sensitivity to the secondary structure. In particular, we find a region near the junction of first and second helix that contains a cluster of water molecules which are slow in motion, characterized by long residence times (of the order of 100 ps or more) and separated by a large free energy barrier from the bulk water. However, these "slow" water molecules constitute only about 5-10% of the total number of hydration layer water molecules. Nevertheless, they play an important role in stabilizing the protein conformation. Water molecules near the third helix (which is the important helix for biological function) are enthalpically least stable and exhibit the fastest dynamics. Interestingly, barrier height distributions of interfacial water are quite broad for water surrounding all the three helices (and the three coils), with the smallest barriers found for those near the helix-3. For the quasi-bound water molecules near the first and second helices, we use well-known Kramers' theory to estimate the residence time from the free energy surface, by estimating the friction along the reaction coordinate from the diffusion coefficient by using Einstein relation. The agreement found is satisfactory. We discuss the possible biological function of these slow, quasi-bound (but transient) water molecules on the surface.

Charge-controlled switchable CO adsorption on FeN4 cluster embedded in graphene

NASA Astrophysics Data System (ADS)

Omidvar, Akbar

2018-02-01

Electrical charging of an FeN4 cluster embedded in graphene (FeN4G) is proposed as an approach for electrocatalytically switchable carbon monoxide (CO) adsorption. Using density functional theory (DFT), we found that the CO molecule is strongly adsorbed on the uncharged FeN4G cluster. Our results show that the adsorption energy of a CO molecule on the FeN4G cluster is dramatically decreased by introducing extra electrons into the cluster. Once the charges are removed, the CO molecule is spontaneously adsorbed on the FeN4G absorbent. In the framework of frontier molecular orbital (FMO) analysis, the enhanced sensitivity and reactivity of the FeN4G cluster towards the CO molecule can be interpreted in terms of interaction between the HOMO of CO molecule and the LUMO of FeN4G cluster. Therefore, this approach promises both facile reversibility and tunable kinetics without the need of specific catalysts. Our study indicates that the FeN4G nanomaterial is an excellent absorbent for controllable and reversible capture and release of the CO.

Vibronic coupling simulations for linear and nonlinear optical processes: Simulation results

NASA Astrophysics Data System (ADS)

Silverstein, Daniel W.; Jensen, Lasse

2012-02-01

A vibronic coupling model based on time-dependent wavepacket approach is applied to simulate linear optical processes, such as one-photon absorbance and resonance Raman scattering, and nonlinear optical processes, such as two-photon absorbance and resonance hyper-Raman scattering, on a series of small molecules. Simulations employing both the long-range corrected approach in density functional theory and coupled cluster are compared and also examined based on available experimental data. Although many of the small molecules are prone to anharmonicity in their potential energy surfaces, the harmonic approach performs adequately. A detailed discussion of the non-Condon effects is illustrated by the molecules presented in this work. Linear and nonlinear Raman scattering simulations allow for the quantification of interference between the Franck-Condon and Herzberg-Teller terms for different molecules.

Biochemical properties of a keratan sulphate/chondroitin sulphate proteoglycan expressed in primate pluripotent stem cells*

PubMed Central

Cooper, Susan; Bennett, William; Andrade, Jessica; Reubinoff, Benjamin E; Thomson, James; Pera, Martin F

2002-01-01

We previously identified a pericellular matrix keratan sulphate/chondroitin sulphate proteoglycan present on the surface of human embryonal carcinoma stem cells, cells whose differentiation mimics early development. Antibodies reactive with various epitopes on this molecule define a cluster of differentiation markers for primate pluripotent stem cells. We describe the purification of a form of this molecule which is secreted or shed into the culture medium. Biochemical analysis of the secreted form of this molecule shows that the monomeric form, whilst containing keratan sulphate, resembles mucins in its structure and its modification with O-linked carbohydrate. Immunofluorescence and immunoblotting data show that monkey and human pluripotent stem cells react with antibodies directed against epitopes on either carbohydrate side chains or the protein core of the molecule. PMID:12033730

Thiol surface complexation on growing CdS clusters

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

Swayambunathan, V.; Hayes, D.; Schmidt, K.H.

1990-05-09

The growth of small CdS colloidal particles has been initiated by pulse radiolytic release of sulfide from thiol (3-mercapto-1,2-propanediol, RSH) in the presence of Cd{sup 2+} ions. The kinetics and stoichiometry of the ensuring reactions were followed by conductivity, absorption spectroscopy, and light-scattering techniques. The final CdS product has been identified by electron diffraction. The formation of Cd-thiolate complexes at the surface of the particles is indicated by conductivity and by energy dispersive analysis of X-ray (EDAX) results. The rate of formation of CdS clusters is strongly pH dependent due to the pH effect on the stability of Dd{sup 2+}/HS{supmore » {minus}} complexes. At low pHs (4.0-5.3) the growth mechanism is proposed to be primarily a cluster-molecule process. At this pH range Cd{sup 2+} ions at the CdS particle surface complex with thiolate ions stronger than in the bulk of the solution. The size control of the particles by thiols is proposed to result from a competition of thiolate ions with HS{sup {minus}} ions for cadmium ions at the surface of the growing particles.« less

Spontaneous Buckling of Lipid Bilayer and Vesicle Budding Induced by Antimicrobial Peptide Magainin 2: A Coarse-Grained Simulation Study

DTIC Science & Technology

2011-05-30

were added to neutralize each system. The GROMACS software package39 was used for simulations. The molecules in this paper refer to the CGMARTINI...accelerated.19 Most of the peptides on the surfaces ended up in clusters containing transmembrane pores, which appeared to perturb the bilayers significantly

MURI Center for Multidimensional Surface-Enhanced Sensing and Spectroscopy

DTIC Science & Technology

2007-06-30

and detection using SERS; new understanding of the electromagnetic enhancement properties of nanohole arrays; new first principles theoretical Page 2...support for the experimental program: 1. Studies of the electrodynamics of molecules adsorbed on anisotropic nanoparticles and nanoholes to determine...nanoparticles. George C. Schatz Electrodynamics of metal nanoparticles, small clusters of nanoparticles and nanoholes . We have performed extensive

Clustering T cell GM1 Lipid Rafts Increases Cellular Resistance to Shear on Fibronectin through Changes in Integrin Affinity and Cytoskeletal Dynamics

PubMed Central

Mitchell, Jason S.; Brown, Wells S.; Woodside, Darren G.; Vanderslice, Peter; McIntyre, Bradley W.

2008-01-01

Lipid rafts are small laterally mobile microdomains that are highly enriched in lymphocyte signaling molecules. GM1 gangliosides are a common lipid raft component and have been shown to be important in many T cell functions. The aggregation of specific GM1 lipid rafts can control many T cell activation events, including their novel association with T cell integrins. We found that clustering GM1 lipid rafts can regulate β1 integrin function. This was apparent through increased resistance to shear flow dependent detachment of T cells adherent to the α4β1 and α5β1 integrin ligand fibronectin (FN). Adhesion strengthening as a result of clustering GM1 enriched lipid rafts correlated with increased cellular rigidity and morphology through the localization of cortical F-actin, the resistance to shear induced cell stretching, and an increase in the surface area and symmetry of the contact area between the cell surface and adhesive substrate. Furthermore, clustering GM1 lipid rafts could initiate integrin “inside-out” signaling mechanisms. This was seen through increased integrin-cytoskeleton associations and enhanced soluble binding of FN and VCAM-1 suggesting the induction of high affinity integrin conformations. The activation of these adhesion strengthening characteristics appear to be specific for the aggregation of GM1 lipid rafts as the aggregation of the heterogeneous raft associated molecule CD59 failed to activate these functions. These findings indicate a novel mechanism to signal to β1 integrins and to activate adhesion strengthening processes. PMID:19139760

Theoretical analysis of hydrogen spillover mechanism on carbon nanotubes

PubMed Central

Juarez-Mosqueda, Rosalba; Mavrandonakis, Andreas; Kuc, Agnieszka B.; Pettersson, Lars G. M.; Heine, Thomas

2015-01-01

The spillover mechanism of molecular hydrogen on carbon nanotubes in the presence of catalytically active platinum clusters was critically and systematically investigated by using density-functional theory. Our simulation model includes a Pt4 cluster for the catalyst nanoparticle and curved and planar circumcoronene for two exemplary single-walled carbon nanotubes (CNT), the (10,10) CNT and one of large diameter, respectively. Our results show that the H2 molecule dissociates spontaneously on the Pt4 cluster. However, the dissociated H atoms have to overcome a barrier of more than 2 eV to migrate from the catalyst to the CNT, even if the Pt4 cluster is at full saturation with six adsorbed and dissociated hydrogen molecules. Previous investigations have shown that the mobility of hydrogen atoms on the CNT surface is hindered by a barrier. We find that instead the Pt4 catalyst may move along the outer surface of the CNT with activation energy of only 0.16 eV, and that this effect offers the possibility of full hydrogenation of the CNT. Thus, although we have not found a low-energy pathway to spillover onto the CNT, we suggest, based on our calculations and calculated data reported in the literature, that in the hydrogen-spillover process the observed saturation of the CNT at hydrogen background pressure occurs through mobile Pt nanoclusters, which move on the substrate more easily than the substrate-chemisorbed hydrogens, and deposit or reattach hydrogens in the process. Initial hydrogenation of the carbon substrate, however, is thermodynamically unfavoured, suggesting that defects should play a significant role. PMID:25699250

Molecular Eigensolution Symmetry Analysis and Fine Structure

PubMed Central

Harter, William G.; Mitchell, Justin C.

2013-01-01

Spectra of high-symmetry molecules contain fine and superfine level cluster structure related to J-tunneling between hills and valleys on rovibronic energy surfaces (RES). Such graphic visualizations help disentangle multi-level dynamics, selection rules, and state mixing effects including widespread violation of nuclear spin symmetry species. A review of RES analysis compares it to that of potential energy surfaces (PES) used in Born–Oppenheimer approximations. Both take advantage of adiabatic coupling in order to visualize Hamiltonian eigensolutions. RES of symmetric and D2 asymmetric top rank-2-tensor Hamiltonians are compared with Oh spherical top rank-4-tensor fine-structure clusters of 6-fold and 8-fold tunneling multiplets. Then extreme 12-fold and 24-fold multiplets are analyzed by RES plots of higher rank tensor Hamiltonians. Such extreme clustering is rare in fundamental bands but prevalent in hot bands, and analysis of its superfine structure requires more efficient labeling and a more powerful group theory. This is introduced using elementary examples involving two groups of order-6 (C6 and D3~C3v), then applied to families of Oh clusters in SF6 spectra and to extreme clusters. PMID:23344041

Ultraviolet and infrared laser-induced fragmentation of free (CF{sub 3}I){sub n} clusters in a molecular beam and (CF{sub 3}I){sub n} clusters inside or on the surface of large (Xe){sub m} clusters

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

Apatin, V. M.; Lokhman, V. N.; Makarov, G. N., E-mail: gmakarov@isan.troitsk.ru

The fragmentation of free homogeneous (CF{sub 3}I){sub n} clusters in a molecular beam (n ≤ 45 is the average number of molecules in the cluster) and (CF{sub 3}I){sub n} clusters inside or on the surface of large (Xe){sub m} clusters (m ≥ 100 is the average number of atoms in the cluster) by ultraviolet and infrared laser radiations has been studied. These three types of (CF{sub 3}I){sub n} clusters are shown to have different stabilities with respect to fragmentation by both ultraviolet and infrared radiations and completely different dependences of the fragmentation probability on the energy of ultraviolet and infraredmore » radiations. When exposed to ultraviolet radiation, the free (CF{sub 3}I){sub n} clusters fragment at comparatively low fluences (Φ{sub UV} ≤ 0.15 J cm{sup −2}) and the weakest energy dependence of the fragmentation probability is observed for them. A stronger energy dependence of the fragmentation probability is observed for the (CF{sub 3}I){sub n} clusters localized inside (Xe){sub m} clusters, and the strongest dependence is observed for the (CF{sub 3}I){sub n} clusters located on the surface of (Xe){sub m} clusters. When the clusters are exposed to infrared radiation, the homogeneous (CF{sub 3}I){sub n} clusters efficiently fragment at low fluences (Φ{sub IR} ≤ 25 mJ cm{sup −2}), higher fluences (Φ{sub IR} ≈ 75 mJ cm{sup −2}) are needed for the fragmentation of the (CF{sub 3}I){sub n} localized inside (Xe){sub m} clusters, and even higher fluences (Φ{sub IR} ≈ 150 mJ cm{sup −2}) are needed for the fragmentation of the (CF{sub 3}I){sub n} clusters located on the surface of (Xe){sub m} clusters. It has been established that small (CF{sub 3}I){sub n} clusters located on the surface of (Xe){sub m} clusters do not fragment up to fluences Φ{sub IR} ≈ 250 mJ cm{sup −2}. The fragmentation efficiency of (CF{sub 3}I){sub n} clusters is shown to be the same (at the same fluence) when they are excited by both pulsed (τ{sub p} ≈ 150 ns) and continuous-wave infrared laser radiations. Possible causes of such a pattern of ultraviolet and infrared laser-induced fragmentation of these clusters are discussed.« less

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

NASA Astrophysics Data System (ADS)

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.

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

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

Negreiros, Fabio R.; Halder, Avik; Yin, Chunrong

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, inmore » 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.« less

Exhaustive comparison and classification of ligand-binding surfaces in proteins

PubMed Central

Murakami, Yoichi; Kinoshita, Kengo; Kinjo, Akira R; Nakamura, Haruki

2013-01-01

Many proteins function by interacting with other small molecules (ligands). Identification of ligand-binding sites (LBS) in proteins can therefore help to infer their molecular functions. A comprehensive comparison among local structures of LBSs was previously performed, in order to understand their relationships and to classify their structural motifs. However, similar exhaustive comparison among local surfaces of LBSs (patches) has never been performed, due to computational complexity. To enhance our understanding of LBSs, it is worth performing such comparisons among patches and classifying them based on similarities of their surface configurations and electrostatic potentials. In this study, we first developed a rapid method to compare two patches. We then clustered patches corresponding to the same PDB chemical component identifier for a ligand, and selected a representative patch from each cluster. We subsequently exhaustively as compared the representative patches and clustered them using similarity score, PatSim. Finally, the resultant PatSim scores were compared with similarities of atomic structures of the LBSs and those of the ligand-binding protein sequences and functions. Consequently, we classified the patches into ∼2000 well-characterized clusters. We found that about 63% of these clusters are used in identical protein folds, although about 25% of the clusters are conserved in distantly related proteins and even in proteins with cross-fold similarity. Furthermore, we showed that patches with higher PatSim score have potential to be involved in similar biological processes. PMID:23934772

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

PubMed

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.

The initial stages of NaCl dissolution: Ion or ion pair solvation?

NASA Astrophysics Data System (ADS)

Klimes, Jiri; Michaelides, Angelos

2009-03-01

The interaction of water with rock salt (NaCl) is important in a wide variety of natural processes and human activities. A lot is known about NaCl dissolution at the macroscopic level but we do not yet have a detailed atomic scale picture of how salt crystals dissolve. Here we report an extensive series of density functional theory, forcefield and molecular dynamics studies of water clusters at flat and defective NaCl surfaces and NaCl clusters. The focus is on answering seemingly elementary questions such as how many water molecules are needed before it becomes favorable to extract an ion or a pair of ions from the crystal or the cluster. It turns out, however, that the answers to these questions are not so straightforward: below a certain number of water molecules (˜ 12) solvation of individual ions is less costly and above this number solvation of ion pairs is favored. These results reveal a hitherto unknown complexity in the NaCl dissolution process born out of a subtle interplay between water-water and water-ion interactions.

Size-Induced Segregation in the Stepwise Microhydration of Hydantoin and Its Role in Proton-Induced Charge Transfer

NASA Astrophysics Data System (ADS)

Calvo, Florent; Bacchus-Montabonel, Marie-Christine

2018-01-01

Recent photochemistry experiments provided evidence for the formation of hydantoin by irradiation of interstellar ice analogues. The significance of these results and the importance of hydantoin in prebiotic chemistry and polypeptide synthesis motivate the present theoretical investigation, in which we analyzed the effects of stepwise hydration on the electronic and thermodynamical properties of the structure of microhydrated hydantoin using a variety of computational approaches. We generally find microhydration to proceed around the hydantoin heterocycle until 5 water molecules are reached, at which stage hydration becomes segregated with a water cluster forming aside the heterocycle. The reactivity of microhydrated hydantoin caused by an impinging proton was evaluated through charge transfer collision cross sections for microhydrated compounds but also for hydantoin on icy grains modeled using a cluster approach mimicking the true hexagonal ice surface. The effects of hydration on charge transfer efficiency are mostly significant when few water molecules are present, and they progressively weaken and stabilize in larger clusters. On the ice substrate, charge transfer essentially contributes to a global increase in the cross sections.

Isotope exchange in reactions between D2O and size-selected ionic water clusters containing pyridine, H+ (pyridine)m(H2O)n.

PubMed

Ryding, Mauritz Johan; Zatula, Alexey S; Andersson, Patrik Urban; Uggerud, Einar

2011-01-28

Pyridine containing water clusters, H(+)(pyridine)(m)(H(2)O)(n), have been studied both experimentally by a quadrupole time-of-flight mass spectrometer and by quantum chemical calculations. In the experiments, H(+)(pyridine)(m)(H(2)O)(n) with m = 1-4 and n = 0-80 are observed. For the cluster distributions observed, there are no magic numbers, neither in the abundance spectra, nor in the evaporation spectra from size selected clusters. Experiments with size-selected clusters H(+)(pyridine)(m)(H(2)O)(n), with m = 0-3, reacting with D(2)O at a center-of-mass energy of 0.1 eV were also performed. The cross-sections for H/D isotope exchange depend mainly on the number of water molecules in the cluster and not on the number of pyridine molecules. Clusters having only one pyridine molecule undergo D(2)O/H(2)O ligand exchange, while H(+)(pyridine)(m)(H(2)O)(n), with m = 2, 3, exhibit significant H/D scrambling. These results are rationalized by quantum chemical calculations (B3LYP and MP2) for H(+)(pyridine)(1)(H(2)O)(n) and H(+)(pyridine)(2)(H(2)O)(n), with n = 1-6. In clusters containing one pyridine, the water molecules form an interconnected network of hydrogen bonds associated with the pyridinium ion via a single hydrogen bond. For clusters containing two pyridines, the two pyridine molecules are completely separated by the water molecules, with each pyridine being positioned diametrically opposite within the cluster. In agreement with experimental observations, these calculations suggest a "see-saw mechanism" for pendular proton transfer between the two pyridines in H(+)(pyridine)(2)(H(2)O)(n) clusters.

Hydration of alcohol clusters in 1-propanol-water mixture studied by quasielastic neutron scattering and an interpretation of anomalous excess partial molar volume.

PubMed

Misawa, M; Inamura, Y; Hosaka, D; Yamamuro, O

2006-08-21

Quasielastic neutron scattering measurements have been made for 1-propanol-water mixtures in a range of alcohol concentration from 0.0 to 0.167 in mole fraction at 25 degrees C. Fraction alpha of water molecules hydrated to fractal surface of alcohol clusters in 1-propanol-water mixture was obtained as a function of alcohol concentration. Average hydration number N(ws) of 1-propanol molecule is derived from the value of alpha as a function of alcohol concentration. By extrapolating N(ws) to infinite dilution, we obtain values of 12-13 as hydration number of isolated 1-propanol molecule. A simple interpretation of structural origin of anomalous excess partial molar volume of water is proposed and as a result a simple equation for the excess partial molar volume is deduced in terms of alpha. Calculated values of the excess partial molar volumes of water and 1-propanol and the excess molar volume of the mixture are in good agreement with experimental values.

Addressing individual metal ion centers in supramolecules by STS

NASA Astrophysics Data System (ADS)

Alam, M. S.; Ako, A. M.; Ruben, M.; Thompson, L. K.; Lehn, J.-M.

2005-03-01

As the information of STM measurements arises from electronic structure, separating information on the topography is not straightforward for complex molecules. Scanning tunneling spectroscopy (STS) measurements give information about the molecular energy levels, which are next to the molecules Fermi level. Using a home built STM working under ambient conditions, we succeeded to combine high resolution topography mapping with simultaneous current-voltage characteristics (STS) measurements on single molecules deposited on highly oriented pyrolytic graphite surfaces. We present our recent results on grid-type molecules [Co4L4] (L=4,6-bis(2',2''-bipyridyl-6-yl)pyrimidine) and [Mn9L6] (L=2POAP-2H) as well as on ring-shaped Fe ion chains [Fe6Cl6L6] (L=1-Ecosyliminodiethanol). Small, regular molecule clusters as well as separated single molecules were observed. We found a rather large contrast at the expected location of the metal centers in our molecules, i.e. the location of the individual metal ions in their organic matrix is directly addressable by STS.

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

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

Fischer, Sean A.; Aprà, Edoardo; Govind, Niranjan

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 withmore » 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.« less

Formation, dissolution and properties of surface nanobubbles

NASA Astrophysics Data System (ADS)

Che, Zhizhao; Theodorakis, Panagiotis E.

2017-02-01

Surface nanobubbles are stable gaseous phases in liquids that form on solid substrates. While their existence has been confirmed, there are many open questions related to their formation and dissolution processes along with their structures and properties, which are difficult to investigate experimentally. To address these issues, we carried out molecular dynamics simulations based on atomistic force fields for systems comprised of water, air (N2 and O2), and a Highly Oriented Pyrolytic Graphite (HOPG) substrate. Our results provide insights into the formation/dissolution mechanisms of nanobubbles and estimates for their density, contact angle, and surface tension. We found that the formation of nanobubbles is driven by an initial nucleation process of air molecules and the subsequent coalescence of the formed air clusters. The clusters form favorably on the substrate, which provides an enhanced stability to the clusters. In contrast, nanobubbles formed in the bulk either move randomly to the substrate and spread or move to the water--air surface and pop immediately. Moreover, nanobubbles consist of a condensed gaseous phase with a surface tension smaller than that of an equivalent system under atmospheric conditions, and contact angles larger than those in the equivalent nanodroplet case. We anticipate that this study will provide useful insights into the physics of nanobubbles and will stimulate further research in the field by using all-atom simulations.

Calcium-decorated carbyne networks as hydrogen storage media.

PubMed

Sorokin, Pavel B; Lee, Hoonkyung; Antipina, Lyubov Yu; Singh, Abhishek K; Yakobson, Boris I

2011-07-13

Among the carbon allotropes, carbyne chains appear outstandingly accessible for sorption and very light. Hydrogen adsorption on calcium-decorated carbyne chain was studied using ab initio density functional calculations. The estimation of surface area of carbyne gives the value four times larger than that of graphene, which makes carbyne attractive as a storage scaffold medium. Furthermore, calculations show that a Ca-decorated carbyne can adsorb up to 6 H(2) molecules per Ca atom with a binding energy of ∼0.2 eV, desirable for reversible storage, and the hydrogen storage capacity can exceed ∼8 wt %. Unlike recently reported transition metal-decorated carbon nanostructures, which suffer from the metal clustering diminishing the storage capacity, the clustering of Ca atoms on carbyne is energetically unfavorable. Thermodynamics of adsorption of H(2) molecules on the Ca atom was also investigated using equilibrium grand partition function.

Second order Møller-Plesset and coupled cluster singles and doubles methods with complex basis functions for resonances in electron-molecule scattering

DOE PAGES

White, Alec F.; Epifanovsky, Evgeny; McCurdy, C. William; ...

2017-06-21

The method of complex basis functions is applied to molecular resonances at correlated levels of theory. Møller-Plesset perturbation theory at second order and equation-of-motion electron attachment coupled-cluster singles and doubles (EOM-EA-CCSD) methods based on a non-Hermitian self-consistent-field reference are used to compute accurate Siegert energies for shape resonances in small molecules including N 2 - , CO - , CO 2 - , and CH 2 O - . Analytic continuation of complex θ-trajectories is used to compute Siegert energies, and the θ-trajectories of energy differences are found to yield more consistent results than those of total energies.more » Furthermore, the ability of such methods to accurately compute complex potential energy surfaces is investigated, and the possibility of using EOM-EA-CCSD for Feshbach resonances is explored in the context of e-helium scattering.« less

Second order Møller-Plesset and coupled cluster singles and doubles methods with complex basis functions for resonances in electron-molecule scattering

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

White, Alec F.; Epifanovsky, Evgeny; McCurdy, C. William

The method of complex basis functions is applied to molecular resonances at correlated levels of theory. Møller-Plesset perturbation theory at second order and equation-of-motion electron attachment coupled-cluster singles and doubles (EOM-EA-CCSD) methods based on a non-Hermitian self-consistent-field reference are used to compute accurate Siegert energies for shape resonances in small molecules including N 2 - , CO - , CO 2 - , and CH 2 O - . Analytic continuation of complex θ-trajectories is used to compute Siegert energies, and the θ-trajectories of energy differences are found to yield more consistent results than those of total energies.more » Furthermore, the ability of such methods to accurately compute complex potential energy surfaces is investigated, and the possibility of using EOM-EA-CCSD for Feshbach resonances is explored in the context of e-helium scattering.« less

Solvent effects on the adsorption and self-organization of Mn12 on Au(111).

PubMed

Pineider, Francesco; Mannini, Matteo; Sessoli, Roberta; Caneschi, Andrea; Barreca, Davide; Armelao, Lidia; Cornia, Andrea; Tondello, Eugenio; Gatteschi, Dante

2007-11-06

A sulfur-containing single molecule magnet, [Mn12O12(O2CC6H4SCH3)16(H2O)4], was assembled from solution on a Au(111) surface affording both submonolayer and monolayer coverages. The adsorbate morphology and the degree of coverage were inspected by scanning tunneling microscopy (STM), while X-ray photoelectron spectroscopy (XPS) allowed the determination of the chemical nature of the adsorbate on a qualitative and quantitative basis. The properties of the adsorbates were found to be strongly dependent on the solvent used to dissolve the magnetic complex. In particular, systems prepared from tetrahydrofuran solutions gave arrays of isolated and partially ordered clusters on the gold substrate, while samples prepared from dichloromethane exhibited a homogeneous monolayer coverage of the whole Au(111) surface. These findings are relevant to the optimization of magnetic addressing of single molecule magnets on surfaces.

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

PubMed

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.

Hydration of excess electrons trapped in charge pockets on molecular surfaces

NASA Astrophysics Data System (ADS)

Jalbout, Abraham F.; Del Castillo, R.; Adamowicz, Ludwik

2007-01-01

In this work we strive to design a novel electron trap located on a molecular surface. The process of electron trapping involves hydration of the trapped electron. Previous calculations on surface electron trapping revealed that clusters of OH groups can form stable hydrogen-bonded networks on one side of a hydrocarbon surface (i.e. cyclohexane sheets), while the hydrogen atoms on the opposite side of the surface form pockets of positive charge that can attract extra negative charge. The excess electron density on such surfaces can be further stabilized by interactions with water molecules. Our calculations show that these anionic systems are stable with respect to vertical electron detachment (VDE).

The energy landscape of glassy dynamics on the amorphous hafnium diboride surface

NASA Astrophysics Data System (ADS)

Nguyen, Duc; Mallek, Justin; Cloud, Andrew N.; Abelson, John R.; Girolami, Gregory S.; Lyding, Joseph; Gruebele, Martin

2014-11-01

Direct visualization of the dynamics of structural glasses and amorphous solids on the sub-nanometer scale provides rich information unavailable from bulk or conventional single molecule techniques. We study the surface of hafnium diboride, a conductive ultrahigh temperature ceramic material that can be grown in amorphous films. Our scanning tunneling movies have a second-to-hour dynamic range and single-point current measurements extend that to the millisecond-to-minute time scale. On the a-HfB2 glass surface, two-state hopping of 1-2 nm diameter cooperatively rearranging regions or "clusters" occurs from sub-milliseconds to hours. We characterize individual clusters in detail through high-resolution (<0.5 nm) imaging, scanning tunneling spectroscopy and voltage modulation, ruling out individual atoms, diffusing adsorbates, or pinned charges as the origin of the observed two-state hopping. Smaller clusters are more likely to hop, larger ones are more likely to be immobile. HfB2 has a very high bulk glass transition temperature Tg, and we observe no three-state hopping or sequential two-state hopping previously seen on lower Tg glass surfaces. The electronic density of states of clusters does not change when they hop up or down, allowing us to calibrate an accurate relative z-axis scale. By directly measuring and histogramming single cluster vertical displacements, we can reconstruct the local free energy landscape of individual clusters, complete with activation barrier height, a reaction coordinate in nanometers, and the shape of the free energy landscape basins between which hopping occurs. The experimental images are consistent with the compact shape of α-relaxors predicted by random first order transition theory, whereas the rapid hopping rate, even taking less confined motion at the surface into account, is consistent with β-relaxations. We make a proposal of how "mixed" features can show up in surface dynamics of glasses.

Simulating Asymmetric Top Impurities in Superfluid Clusters: A para-Water Dopant in para-Hydrogen.

PubMed

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

2013-01-03

We present the first simulation study of bosonic clusters doped with an asymmetric top molecule. The path-integral Monte Carlo method with the latest methodological advance in treating rigid-body rotation [Noya, E. G.; Vega, C.; McBride, C. J. Chem. Phys.2011, 134, 054117] is employed to study a para-water impurity in para-hydrogen clusters with up to 20 para-hydrogen molecules. The growth pattern of the doped clusters is similar in nature to that of pure clusters. The para-water molecule appears to rotate freely in the cluster. The presence of para-water substantially quenches the superfluid response of para-hydrogen with respect to the space-fixed frame.

Theoretical study of the H2 reaction with a Pt4 (111) cluster

NASA Astrophysics Data System (ADS)

Cruz, A.; Bertin, V.; Poulain, E.; Benitez, J. I.; Castillo, S.

2004-04-01

The Cs symmetry reaction of the H2 molecule on a Pt4 (111) clusters, has been studied using ab initio multiconfiguration self-consistent field plus extensive multireference configuration interaction variational and perturbative calculations. The H2 interaction by the vertex and by the base of a tetrahedral Pt4 cluster were studied in ground and excited triplet and singlet states (closed and open shells), where the reaction curves are obtained through many avoided crossings. The Pt4 cluster captures and activates the hydrogen molecule; it shows a similar behavior compared with other Ptn (n=1,2,3) systems. The Pt4 cluster in their lowest five open and closed shell electronic states: 3B2, 1B2, 1A1 3A1, 1A1, respectively, may capture and dissociate the H2 molecule without activation barriers for the hydrogen molecule vertex approach. For the threefolded site reaction, i.e., by the base, the situation is different, the hydrogen adsorption presents some barriers. The potential energy minima occur outside and inside the cluster, with strong activation of the H-H bond. In all cases studied, the Pt4 cluster does not absorb the hydrogen molecule.

Ab Initio Study of KCl and AgCl Clusters.

NASA Astrophysics Data System (ADS)

McKeough, James; Hira, Ajit; Cathey, Tommy; Valdez, Alexandra

This paper presents a theoretical study of molecular clusters that examines the chemical and physical properties of small KnCln and AgnCln clusters (n = 2 - 24). Due to combinations of attractive and repulsive long-range forces, such clusters exhibit structural and dynamical behavior different from that of homogeneous clusters. The potentially important role of these molecular species in biochemical and medicinal processes is widely known. This work applies the hybrid ab initio methods to derive the different alkali-halide (MnHn) geometries. Of particular interest is the competition between hexagonal ring geometries and rock salt structures. Electronic energies, rotational constants, dipole moments, and vibrational frequencies for these geometries are calculated. Magic numbers for cluster stability are identified and are related to the property of cluster compactness. Mapping of the singlet, triplet, and quintet, potential energy surfaces is performed. Calculations were performed to examine the interactions of these clusters with some atoms and molecules of biological interest, including O, O2, and Fe. Potential design of new medicinal drugs is explored. We will also investigate model and material dependence of the results. AMP program of the National Science Foundation.

Application of chiral critical clusters to assymetric synthesis

DOEpatents

Ferrieri, Richard A.

2002-01-01

Disclosed is a composition, a method of making and a method of using critical clusters for asymmetric synthesis using substantially optically-pure chiral solvent molecules in a supercritical fluid. The solvent molecules are capable of forming a multipoint hydrogen bonded solvate as they encage at least one solute molecule. The encaged solute molecule is capable of reacting to form an optically active chiral center. In another aspect, there is disclosed a method of directing the position of bonding between a solute molecule and a ligand involving encaging the solute molecule and the ligand with polar solvent molecules in a supercritical fluid under conditions of temperature and pressure sufficient to change electric charge distribution in the solute molecule. In yet another aspect, disclosed is a method of making pharmaceutical compounds involving encaging a solute molecule, which is capable of forming a chiral center, and a ligand with polar solvent molecules in a supercritical fluid under conditions of temperature and pressure sufficient to change electric charge distribution of the solute molecule. The solute molecule and ligand are then reacted whereby the ligand bonds to the solute molecule forming a chiral center. Also disclosed is a method for racemic resolution using critical clusters involving encaging racemic mixtures of solute molecules with substantially optically-pure chiral solvent molecules in a supercritical fluid under conditions of temperature and pressure sufficient to form critical clusters. The solvent molecules are capable of multipoint hydrogen bonding with the solute molecules. The encaged solute molecules are then nonenzymatically reacted to enhance the optical purity of the solute molecules.

Lasers '81

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

Collins, C.B.

1982-01-01

Progress in lasers is discussed. The subjects addressed include: excimer lasers, surface spectroscopy, modern laser spectroscopy, free electron lasers, cavities and propagation, lasers in medicine, X-ray and gamma ray lasers, laser spectroscopy of small molecules and clusters, optical bistability, excitons, nonlinear optics in the X-ray and gamma ray regions, collective atomic phenomena, tunable IR lasers, far IR/submillimeter lasers, and laser-assisted collisions. Also treated are: special applications, multiphoton processes in atoms and small molecules, nuclear pumped lasers, material processing and applications, polarization, high energy lasers, laser chemistry, IR molecular lasers, laser applications of collision and dissociation phenomena, solid state laser materials,more » phase conjugation, advances in laser technology for fusion, metal vapor lasers, picosecond phenomena, laser ranging and geodesy, and laser photochemistry of complex molecules.« less

C{sub 60}-dyad aggregates: Self-organized structures in aqueous solutions

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

Guskova, O. A., E-mail: guskova@ipfdd.de, E-mail: s.raovaranasi@uq.edu.au; Varanasi, S. R., E-mail: guskova@ipfdd.de, E-mail: s.raovaranasi@uq.edu.au; Sommer, J.-U.

2014-10-14

Extensive full-atomistic molecular dynamics simulations are performed to study the self-organization of C{sub 60}-fullerene dyad molecules in water, namely phenyl-C{sub 61}-butyric acid methyl ester and fulleropyrrolidines, which have two elements of ordering, the hydrophobic fullerene cage and the hydrophilic/ionic group. While pristine fullerene or phenyl-C{sub 61}-butyric acid methyl ester forms spherical droplets in order to minimize the surface tension, the amphiphilic nature of charged solute molecules leads to the formation of supramolecular assemblies having cylindrical shape driven by charge repulsion between the ionic groups located on the surface of the aggregates. We show that formation of non-spherical micelles is themore » geometrical consequence if the fullerene derivatives are considered as surfactants where the ionized groups are only hydrophilic unit. The agglomeration behavior of fullerenes is evaluated by determining sizes of the clusters, solvent accessible surface areas, and shape parameters. By changing the size of the counterions from chloride over iodide to perchlorate we find a thickening of the cylinder-like structures which can be explained by stronger condensation of larger ions and thus partial screening of the charge repulsion on the cluster surface. The reason for the size dependence of counterion condensation is the formation of a stronger hydration shell in case of small ions which in turn are repelled from the fullerene aggregates. Simulations are also in good agreement with the experimentally observed morphologies of decorated C{sub 60}-nanoparticles.« less

Molecular codes for neuronal individuality and cell assembly in the brain

PubMed Central

Yagi, Takeshi

2012-01-01

The brain contains an enormous, but finite, number of neurons. The ability of this limited number of neurons to produce nearly limitless neural information over a lifetime is typically explained by combinatorial explosion; that is, by the exponential amplification of each neuron's contribution through its incorporation into “cell assemblies” and neural networks. In development, each neuron expresses diverse cellular recognition molecules that permit the formation of the appropriate neural cell assemblies to elicit various brain functions. The mechanism for generating neuronal assemblies and networks must involve molecular codes that give neurons individuality and allow them to recognize one another and join appropriate networks. The extensive molecular diversity of cell-surface proteins on neurons is likely to contribute to their individual identities. The clustered protocadherins (Pcdh) is a large subfamily within the diverse cadherin superfamily. The clustered Pcdh genes are encoded in tandem by three gene clusters, and are present in all known vertebrate genomes. The set of clustered Pcdh genes is expressed in a random and combinatorial manner in each neuron. In addition, cis-tetramers composed of heteromultimeric clustered Pcdh isoforms represent selective binding units for cell-cell interactions. Here I present the mathematical probabilities for neuronal individuality based on the random and combinatorial expression of clustered Pcdh isoforms and their formation of cis-tetramers in each neuron. Notably, clustered Pcdh gene products are known to play crucial roles in correct axonal projections, synaptic formation, and neuronal survival. Their molecular and biological features induce a hypothesis that the diverse clustered Pcdh molecules provide the molecular code by which neuronal individuality and cell assembly permit the combinatorial explosion of networks that supports enormous processing capability and plasticity of the brain. PMID:22518100

Self-assembly of (perfluoroalkyl)alkanes on a substrate surface from solutions in supercritical carbon dioxide.

PubMed

Gallyamov, Marat O; Mourran, Ahmed; Tartsch, Bernd; Vinokur, Rostislav A; Nikitin, Lev N; Khokhlov, Alexei R; Schaumburg, Kjeld; Möller, Martin

2006-06-14

Toroidal self-assembled structures of perfluorododecylnonadecane and perfluorotetradecyloctadecane have been deposited on mica and highly oriented pyrolytic graphite surfaces by exposure of the substrates to solutions of the (pefluoroalkyl)alkanes in supercritical carbon dioxide. Scanning force microscopy (SFM) images have displayed a high degree of regularity of these self-assembled nanoobjects regarding size, shape, and packing in a monolayer. Analysis of SFM images allowed us to estimate that each toroidal domain has an outer diameter of about 50 nm and consists of several thousands of molecules. We propose a simple model explaining the clustering of the molecules to objects with a finite size. The model based on the close-packing principles predicts formation of toroids, whose size is determined by the molecular geometry. Here, we consider the amphiphilic nature of the (perfluoroalkyl)alkane molecules in combination with incommensurable packing parameters of the alkyl- and the perfluoralkyl-segments to be a key factor for such a self-assembly.

Exploring the possibility to store the mixed oxygen-hydrogen cluster in clathrate hydrate in molar ratio 1:2 (O2+2H2).

PubMed

Qin, Yan; Du, Qi-Shi; Xie, Neng-Zhong; Li, Jian-Xiu; Huang, Ri-Bo

2017-05-01

An interesting possibility is explored: storing the mixture of oxygen and hydrogen in clathrate hydrate in molar ratio 1:2. The interaction energies between oxygen, hydrogen, and clathrate hydrate are calculated using high level quantum chemical methods. The useful conclusion points from this study are summarized as follows. (1) The interaction energies of oxygen-hydrogen mixed cluster are larger than the energies of pure hydrogen molecular cluster. (2) The affinity of oxygen molecules with water molecules is larger than that of the hydrogen molecules with water molecules. (3) The dimension of O 2 -2H 2 interaction structure is smaller than the dimension of CO 2 -2H 2 interaction structure. (4) The escaping energy of oxygen molecules from the hydrate cell is larger than that of the hydrogen molecules. (5) The high affinity of the oxygen molecules with both the water molecules and the hydrogen molecules may promote the stability of oxygen-hydrogen mixture in the clathrate hydrate. Therefore it is possible to store the mixed (O 2 +2H 2 ) cluster in clathrate hydrate. Copyright © 2017 Elsevier Inc. All rights reserved.

Conservative mutation Met8 --> Leu affects the folding process and structural stability of squash trypsin inhibitor CMTI-I.

PubMed Central

Zhukov, I.; Jaroszewski, L.; Bierzyński, A.

2000-01-01

Protein molecules can accommodate a large number of mutations without noticeable effects on their stability and folding kinetics. On the other hand, some mutations can have quite strong effects on protein conformational properties. Such mutations either destabilize secondary structures, e.g., alpha-helices, are incompatible with close packing of protein hydrophobic cores, or lead to disruption of some specific interactions such as disulfide cross links, salt bridges, hydrogen bonds, or aromatic-aromatic contacts. The Met8 --> Leu mutation in CMTI-I results in significant destabilization of the protein structure. This effect could hardly be expected since the mutation is highly conservative, and the side chain of residue 8 is situated on the protein surface. We show that the protein destabilization is caused by rearrangement of a hydrophobic cluster formed by side chains of residues 8, Ile6, and Leu17 that leads to partial breaking of a hydrogen bond formed by the amide group of Leu17 with water and to a reduction of a hydrophobic surface buried within the cluster. The mutation perturbs also the protein folding. In aerobic conditions the reduced wild-type protein folds effectively into its native structure, whereas more then 75% of the mutant molecules are trapped in various misfolded species. The main conclusion of this work is that conservative mutations of hydrophobic residues can destabilize a protein structure even if these residues are situated on the protein surface and partially accessible to water. Structural rearrangement of small hydrophobic clusters formed by such residues can lead to local changes in protein hydration, and consequently, can affect considerably protein stability and folding process. PMID:10716179

Distribution of a Glycosylphosphatidylinositol-anchored Protein at the Apical Surface of MDCK Cells Examined at a Resolution of <100 Å Using Imaging Fluorescence Resonance Energy Transfer

PubMed Central

Kenworthy, A.K.; Edidin, M.

1998-01-01

Membrane microdomains (“lipid rafts”) enriched in glycosylphosphatidylinositol (GPI)-anchored proteins, glycosphingolipids, and cholesterol have been implicated in events ranging from membrane trafficking to signal transduction. Although there is biochemical evidence for such membrane microdomains, they have not been visualized by light or electron microscopy. To probe for microdomains enriched in GPI- anchored proteins in intact cell membranes, we used a novel form of digital microscopy, imaging fluorescence resonance energy transfer (FRET), which extends the resolution of fluorescence microscopy to the molecular level (<100 Å). We detected significant energy transfer between donor- and acceptor-labeled antibodies against the GPI-anchored protein 5′ nucleotidase (5′ NT) at the apical membrane of MDCK cells. The efficiency of energy transfer correlated strongly with the surface density of the acceptor-labeled antibody. The FRET data conformed to theoretical predictions for two-dimensional FRET between randomly distributed molecules and were inconsistent with a model in which 5′ NT is constitutively clustered. Though we cannot completely exclude the possibility that some 5′ NT is in clusters, the data imply that most 5′ NT molecules are randomly distributed across the apical surface of MDCK cells. These findings constrain current models for lipid rafts and the membrane organization of GPI-anchored proteins. PMID:9660864

Endocytosis of GPI-anchored proteins in human lymphocytes: role of glycolipid-based domains, actin cytoskeleton, and protein kinases

PubMed Central

1996-01-01

GPI-anchored surface proteins mediate many important functions, including transport, signal transduction, adhesion, and protection against complement. They cluster into glycolipid-based membrane domains and caveolae, plasmalemmal vesicles involved in the transcytosis and endocytosis of these surface proteins. However, in lymphocytes, neither the characteristic flask shaped caveolae nor caveolin, a transmembrane protein typical of caveolae, have been observed. Here, we show that the GPI-anchored CD59 molecule on Jurkat T cells is internalized after cross-linking, a process inhibited by nystatin, a sterol chelating agent. Clustered CD59 molecules mostly accumulate in non-coated invaginations of the lymphocyte membrane before endocytosis, in marked contrast with the pattern of CD3-TCR internalization. Cytochalasin H blocked CD59 internalization in lymphocytes, but neither CD3 internalization nor transferrin uptake. Confocal microscopy analysis of F-actin distribution within lymphocytes showed that CD59 clusters were associated with patches of polymerized actin. Also, we found that internalization of CD59 was prevented by the protein kinase C inhibitor staurosporine and by the protein kinase A activator forskolin. Thus, in lymphocytes, as in other cell types, glycolipid-based domains provide sites of integration of signaling pathways involved in GPI-anchored protein endocytosis. This process, which is regulated by both protein kinase C and A activity, is tightly controlled by the dynamic organization of actin cytoskeleton, and may be critical for polarized contacts of circulating cells. PMID:8666664

Lipid Clustering Correlates with Membrane Curvature as Revealed by Molecular Simulations of Complex Lipid Bilayers

PubMed Central

Koldsø, Heidi; Shorthouse, David; Hélie, Jean; Sansom, Mark S. P.

2014-01-01

Cell membranes are complex multicomponent systems, which are highly heterogeneous in the lipid distribution and composition. To date, most molecular simulations have focussed on relatively simple lipid compositions, helping to inform our understanding of in vitro experimental studies. Here we describe on simulations of complex asymmetric plasma membrane model, which contains seven different lipids species including the glycolipid GM3 in the outer leaflet and the anionic lipid, phosphatidylinositol 4,5-bisphophate (PIP2), in the inner leaflet. Plasma membrane models consisting of 1500 lipids and resembling the in vivo composition were constructed and simulations were run for 5 µs. In these simulations the most striking feature was the formation of nano-clusters of GM3 within the outer leaflet. In simulations of protein interactions within a plasma membrane model, GM3, PIP2, and cholesterol all formed favorable interactions with the model α-helical protein. A larger scale simulation of a model plasma membrane containing 6000 lipid molecules revealed correlations between curvature of the bilayer surface and clustering of lipid molecules. In particular, the concave (when viewed from the extracellular side) regions of the bilayer surface were locally enriched in GM3. In summary, these simulations explore the nanoscale dynamics of model bilayers which mimic the in vivo lipid composition of mammalian plasma membranes, revealing emergent nanoscale membrane organization which may be coupled both to fluctuations in local membrane geometry and to interactions with proteins. PMID:25340788

Lipid clustering correlates with membrane curvature as revealed by molecular simulations of complex lipid bilayers.

PubMed

Koldsø, Heidi; Shorthouse, David; Hélie, Jean; Sansom, Mark S P

2014-10-01

Cell membranes are complex multicomponent systems, which are highly heterogeneous in the lipid distribution and composition. To date, most molecular simulations have focussed on relatively simple lipid compositions, helping to inform our understanding of in vitro experimental studies. Here we describe on simulations of complex asymmetric plasma membrane model, which contains seven different lipids species including the glycolipid GM3 in the outer leaflet and the anionic lipid, phosphatidylinositol 4,5-bisphophate (PIP2), in the inner leaflet. Plasma membrane models consisting of 1500 lipids and resembling the in vivo composition were constructed and simulations were run for 5 µs. In these simulations the most striking feature was the formation of nano-clusters of GM3 within the outer leaflet. In simulations of protein interactions within a plasma membrane model, GM3, PIP2, and cholesterol all formed favorable interactions with the model α-helical protein. A larger scale simulation of a model plasma membrane containing 6000 lipid molecules revealed correlations between curvature of the bilayer surface and clustering of lipid molecules. In particular, the concave (when viewed from the extracellular side) regions of the bilayer surface were locally enriched in GM3. In summary, these simulations explore the nanoscale dynamics of model bilayers which mimic the in vivo lipid composition of mammalian plasma membranes, revealing emergent nanoscale membrane organization which may be coupled both to fluctuations in local membrane geometry and to interactions with proteins.

Photoionization of rare gas clusters

NASA Astrophysics Data System (ADS)

Zhang, Huaizhen

This thesis concentrates on the study of photoionization of van der Waals clusters with different cluster sizes. The goal of the experimental investigation is to understand the electronic structure of van der Waals clusters and the electronic dynamics. These studies are fundamental to understand the interaction between UV-X rays and clusters. The experiments were performed at the Advanced Light Source at Lawrence Berkeley National Laboratory. The experimental method employs angle-resolved time-of-flight photoelectron spectrometry, one of the most powerful methods for probing the electronic structure of atoms, molecules, clusters and solids. The van der Waals cluster photoionization studies are focused on probing the evolution of the photoelectron angular distribution parameter as a function of photon energy and cluster size. The angular distribution has been known to be a sensitive probe of the electronic structure in atoms and molecules. However, it has not been used in the case of van der Waals clusters. We carried out outer-valence levels, inner-valence levels and core-levels cluster photoionization experiments. Specifically, this work reports on the first quantitative measurements of the angular distribution parameters of rare gas clusters as a function of average cluster sizes. Our findings for xenon clusters is that the overall photon-energy-dependent behavior of the photoelectrons from the clusters is very similar to that of the corresponding free atoms. However, distinct differences in the angular distribution point at cluster-size-dependent effects were found. For krypton clusters, in the photon energy range where atomic photoelectrons have a high angular anisotropy, our measurements show considerably more isotropic angular distributions for the cluster photoelectrons, especially right above the 3d and 4p thresholds. For the valence electrons, a surprising difference between the two spin-orbit components was found. For argon clusters, we found that the angular distribution parameter values of the two-spin-orbit components from Ar 2p clusters are slightly different. When comparing the beta values for Ar between atoms and clusters, we found different results between Ar 3s atoms and clusters, and between Ar 3p atoms and clusters. Argon cluster resonance from surface and bulk were also measured. Furthermore, the angular distribution parameters of Ar cluster photoelectrons and Ar atom photoelectrons in the 3s → np ionization region were obtained.

Single molecule magnets with protective ligand shells on gold and titanium dioxide surfaces: In situ electrospray deposition and x-ray absorption spectroscopy

NASA Astrophysics Data System (ADS)

Handrup, Karsten; Richards, Victoria J.; Weston, Matthew; Champness, Neil R.; O'Shea, James N.

2013-10-01

Two single molecule magnets based on the dodecamanganese (III, IV) cluster with either benzoate or terphenyl-4-carboxylate ligands, have been studied on the Au(111) and rutile TiO2(110) surfaces. We have used in situ electrospray deposition to produce a series of surface coverages from a fraction of a monolayer to multilayer films in both cases. X-ray absorption spectroscopy measured at the Mn L-edge (Mn 2p) has been used to study the effect of adsorption on the oxidation states of the manganese atoms in the core. In the case of the benzoate-functionalised complex reduction of the manganese metal centres is observed due to the interaction of the manganese core with the underlying surface. In the case of terphenyl-4-carboxylate, the presence of this much larger ligand prevents the magnetic core from interacting with either the gold or the titanium dioxide surfaces and the characteristic Mn3+ and Mn4+ oxidation states necessary for magnetic behaviour are preserved.

Absolute surface energy calculations of Wurtzite (0001)/(000-1): a study of ZnO and GaN

NASA Astrophysics Data System (ADS)

Zhang, Jingzhao; Zhang, Yiou; Tse, Kinfai; Deng, Bei; Xu, Hu; Zhu, Junyi

The accurate absolute surface energies of (0001)/(000-1) surfaces of wurtzite structures are crucial in determining the thin film growth mode of important energy materials. However, the surface energies still remain to be solved due to the intrinsic difficulty of calculating dangling bond energy of asymmetrically bonded surface atoms. We used a pseudo-hydrogen passivation method to estimate the dangling bond energy and calculate the polar surfaces of ZnO and GaN. The calculations were based on the pseudo chemical potentials obtained from a set of tetrahedral clusters or simple pseudo-molecules, using density functional theory approaches, for both GGA and HSE. And the surface energies of (0001)/(000-1) surfaces of wurtzite ZnO and GaN we obtained showed relatively high self-consistencies. A wedge structure calculation with a new bottom surface passivation scheme of group I and group VII elements was also proposed and performed to show converged absolute surface energy of wurtzite ZnO polar surfaces. Part of the computing resources was provided by the High Performance Cluster Computing Centre, Hong Kong Baptist University. This work was supported by the start-up funding and direct Grant with the Project code of 4053134 at CUHK.

High-throughput platform for the discovery of elicitors of silent bacterial gene clusters.

PubMed

Seyedsayamdost, Mohammad R

2014-05-20

Over the past decade, bacterial genome sequences have revealed an immense reservoir of biosynthetic gene clusters, sets of contiguous genes that have the potential to produce drugs or drug-like molecules. However, the majority of these gene clusters appear to be inactive for unknown reasons prompting terms such as "cryptic" or "silent" to describe them. Because natural products have been a major source of therapeutic molecules, methods that rationally activate these silent clusters would have a profound impact on drug discovery. Herein, a new strategy is outlined for awakening silent gene clusters using small molecule elicitors. In this method, a genetic reporter construct affords a facile read-out for activation of the silent cluster of interest, while high-throughput screening of small molecule libraries provides potential inducers. This approach was applied to two cryptic gene clusters in the pathogenic model Burkholderia thailandensis. The results not only demonstrate a prominent activation of these two clusters, but also reveal that the majority of elicitors are themselves antibiotics, most in common clinical use. Antibiotics, which kill B. thailandensis at high concentrations, act as inducers of secondary metabolism at low concentrations. One of these antibiotics, trimethoprim, served as a global activator of secondary metabolism by inducing at least five biosynthetic pathways. Further application of this strategy promises to uncover the regulatory networks that activate silent gene clusters while at the same time providing access to the vast array of cryptic molecules found in bacteria.

Structure of a Premicellar Complex of Alkyl Sulfates with the Interfacial Binding Surfaces of 4 Subunits of Phospholipase A2✰

PubMed Central

Pan, Ying H.; Bahnson, Brian J.

2010-01-01

The properties of three discrete premicellar complexes (E1#, E2#, E3#) of pig pancreatic group-IB secreted phospholipase A2 (sPLA2) with monodisperse alkyl sulfates has been characterized [Berg, O. G., et al., Biochemistry 43, 7999–8013, 2004]. Here we have solved the 2.7 Å crystal structure of group-IB sPLA2 complexed with 12 molecules of octyl sulfate (C8S) in a form consistent with a tetrameric oligomeric that exists during the E1# phase of premicellar complexes. The alkyl tails of the C8S molecules are centered in the middle of the tetrameric cluster of sPLA2 subunits. Three of the four sPLA2 subunits also contain a C8S molecule in the active site pocket. The sulfate oxygen of a C8S ligand is complexed to the active site calcium in 3 of the 4 protein active sites. The interactions of the alkyl sulfate head group with Arg-6 and Lys-10, as well as the backbone amide of Met-20, are analogous to those observed in the previously solved sPLA2 crystal structures with bound phosphate and sulfate anions. The cluster of three anions found in the present structure is postulated to be the site for nucleating the binding of anionic amphiphiles to the interfacial surface of the protein, and therefore this binding interaction has implications for interfacial activation of the enzyme. PMID:20302975

Long-Range Capture and Delivery of Water-Dispersed Nano-objects by Microbubbles Generated on 3D Plasmonic Surfaces.

PubMed

Tantussi, Francesco; Messina, Gabriele C; Capozza, Rosario; Dipalo, Michele; Lovato, Laura; De Angelis, Francesco

2018-05-22

The possibility of investigating small amounts of molecules, moieties, or nano-objects dispersed in solution constitutes a central step for various application areas in which high sensitivity is necessary. Here, we show that the rapid expansion of a water bubble can act as a fast-moving net for molecules or nano-objects, collecting the floating objects in the surrounding medium in a range up to 100 μm. Thanks to an engineered 3D patterning of the substrate, the collapse of the bubble could be guided toward a designed area of the surface with micrometric precision. Thus, a locally confined high density of particles is obtained, ready for evaluation by most optical/spectroscopic detection schemes. One of the main relevant strengths of the long-range capture and delivery method is the ability to increase, by a few orders of magnitude, the local density of particles with no changes in their physiological environment. The bubble is generated by an ultrafast IR laser pulse train focused on a resonant plasmonic antenna; due to the excitation process, the technique is trustworthy and applicable to biological samples. We have tested the reliabilities of the process by concentrating highly dispersed fluorescence molecules and fluorescent beads. Lastly, as an ultimate test, we have applied the bubble clustering method on nanosized exosome vesicles dispersed in water; due to the clustering effect, we were able to effectively perform Raman spectroscopy on specimens that were otherwise extremely difficult to measure.

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

NASA Astrophysics Data System (ADS)

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.

Composition Formulas of Inorganic Compounds in Terms of Cluster Plus Glue Atom Model.

PubMed

Ma, Yanping; Dong, Dandan; Wu, Aimin; Dong, Chuang

2018-01-16

The present paper attempts to identify the molecule-like structural units in inorganic compounds, by applying the so-called "cluster plus glue atom model". This model, originating from metallic glasses and quasi-crystals, describes any structure in terms of a nearest-neighbor cluster and a few outer-shell glue atoms, expressed in the cluster formula [cluster](glue atoms). Similar to the case for normal molecules where the charge transfer occurs within the molecule to meet the commonly known octet electron rule, the octet state is reached after matching the nearest-neighbor cluster with certain outer-shell glue atoms. These kinds of structural units contain information on local atomic configuration, chemical composition, and electron numbers, just as for normal molecules. It is shown that the formulas of typical inorganic compounds, such as fluorides, oxides, and nitrides, satisfy a similar octet electron rule, with the total number of valence electrons per unit formula being multiples of eight.

A machine learning approach to graph-theoretical cluster expansions of the energy of adsorbate layers

NASA Astrophysics Data System (ADS)

Vignola, Emanuele; Steinmann, Stephan N.; Vandegehuchte, Bart D.; Curulla, Daniel; Stamatakis, Michail; Sautet, Philippe

2017-08-01

The accurate description of the energy of adsorbate layers is crucial for the understanding of chemistry at interfaces. For heterogeneous catalysis, not only the interaction of the adsorbate with the surface but also the adsorbate-adsorbate lateral interactions significantly affect the activation energies of reactions. Modeling the interactions of the adsorbates with the catalyst surface and with each other can be efficiently achieved in the cluster expansion Hamiltonian formalism, which has recently been implemented in a graph-theoretical kinetic Monte Carlo (kMC) scheme to describe multi-dentate species. Automating the development of the cluster expansion Hamiltonians for catalytic systems is challenging and requires the mapping of adsorbate configurations for extended adsorbates onto a graphical lattice. The current work adopts machine learning methods to reach this goal. Clusters are automatically detected based on formalized, but intuitive chemical concepts. The corresponding energy coefficients for the cluster expansion are calculated by an inversion scheme. The potential of this method is demonstrated for the example of ethylene adsorption on Pd(111), for which we propose several expansions, depending on the graphical lattice. It turns out that for this system, the best description is obtained as a combination of single molecule patterns and a few coupling terms accounting for lateral interactions.

A highly sensitive nanoscale pH-sensor using Au nanoparticles linked by a multifunctional Raman-active reporter molecule

NASA Astrophysics Data System (ADS)

Lawson, Latevi S.; Chan, James W.; Huser, Thomas

2014-06-01

Chemical sensing on the nanoscale has been breaking new ground since the discovery of surface enhanced Raman scattering (SERS). For nanoparticles, controlled particle aggregation is necessary to achieve the largest SERS enhancements. Therefore, aggregating agents such as salts or linker molecules are used in conjunction with chemically sensitive reporters in order to develop robust environmentally sensitive SERS probes. While salt-induced colloidal nanosphere aggregates have produced robust SERS signals, their variability in aggregate size contributes significantly to poor SERS signal reproducibility, which can complicate their use in in vitro cellular studies. Such systems often also lack reproducibility in spectral measurements between different nanoparticle clusters. Preaggregation of colloids via linkers followed by surface functionalization with reporter molecules results in the linker occupying valuable SERS hotspot volume which could otherwise be utilized by additional reporter molecules. Ideally, both functionalities should be obtained from a single molecule. Here, we report the use of 3,5-dimercaptobenzoic acid, a single multifunctional molecule that creates SERS hotspots via the controlled aggregation of nanoparticles, and also reports pH values. We show that 3,5-dimercaptobenzoic acid bound to Au nanospheres results in an excellent pH nanoprobe, producing very robust, and highly reproducible SERS signals that can report pH across the entire physiological range with excellent pH resolution. To demonstrate the efficacy of our novel pH reporters, these probes were also used to image both the particle and pH distribution in the cytoplasm of human induced pluripotent stem cells (hiPSCs).Chemical sensing on the nanoscale has been breaking new ground since the discovery of surface enhanced Raman scattering (SERS). For nanoparticles, controlled particle aggregation is necessary to achieve the largest SERS enhancements. Therefore, aggregating agents such as salts or linker molecules are used in conjunction with chemically sensitive reporters in order to develop robust environmentally sensitive SERS probes. While salt-induced colloidal nanosphere aggregates have produced robust SERS signals, their variability in aggregate size contributes significantly to poor SERS signal reproducibility, which can complicate their use in in vitro cellular studies. Such systems often also lack reproducibility in spectral measurements between different nanoparticle clusters. Preaggregation of colloids via linkers followed by surface functionalization with reporter molecules results in the linker occupying valuable SERS hotspot volume which could otherwise be utilized by additional reporter molecules. Ideally, both functionalities should be obtained from a single molecule. Here, we report the use of 3,5-dimercaptobenzoic acid, a single multifunctional molecule that creates SERS hotspots via the controlled aggregation of nanoparticles, and also reports pH values. We show that 3,5-dimercaptobenzoic acid bound to Au nanospheres results in an excellent pH nanoprobe, producing very robust, and highly reproducible SERS signals that can report pH across the entire physiological range with excellent pH resolution. To demonstrate the efficacy of our novel pH reporters, these probes were also used to image both the particle and pH distribution in the cytoplasm of human induced pluripotent stem cells (hiPSCs). Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr06277e

Structural features of small benzene clusters (C6H6)n (n ≤ 30) as investigated with the all-atom OPLS potential.

PubMed

Takeuchi, Hiroshi

2012-10-18

The structures of the simplest aromatic clusters, benzene clusters (C(6)H(6))(n), are not well elucidated. In the present study, benzene clusters (C(6)H(6))(n) (n ≤ 30) were investigated with the all-atom optimized parameters for liquid simulation (OPLS) potential. The global minima and low-lying minima of the benzene clusters were searched with the heuristic method combined with geometrical perturbations. The structural features and growth sequence of the clusters were examined by carrying out local structure analyses and structural similarity evaluation with rotational constants. Because of the anisotropic interaction between the benzene molecules, the local structures consisting of 13 molecules are considerably deviated from regular icosahedron, and the geometries of some of the clusters are inconsistent with the shapes constructed by the interior molecules. The distribution of the angle between the lines normal to two neighboring benzene rings is anisotropic in the clusters, whereas that in the liquid benzene is nearly isotropic. The geometries and energies of the low-lying configurations and the saddle points between them suggest that most of the configurations previously detected in supersonic expansions take different orientations for one to four neighboring molecules.

Spin-driven structural effects in alkali doped (4)He clusters from quantum calculations.

PubMed

Bovino, S; Coccia, E; Bodo, E; Lopez-Durán, D; Gianturco, F A

2009-06-14

In this paper, we carry out variational Monte Carlo and diffusion Monte Carlo (DMC) calculations for Li(2)((1)Sigma(g) (+))((4)He)(N) and Li(2)((3)Sigma(u) (+))((4)He)(N) with N up to 30 and discuss in detail the results of our computations. After a comparison between our DMC energies with the "exact" discrete variable representation values for the species with one (4)He, in order to test the quality of our computations at 0 K, we analyze the structural features of the whole range of doped clusters. We find that both species reside on the droplet surface, but that their orientation is spin driven, i.e., the singlet molecule is perpendicular and the triplet one is parallel to the droplet's surface. We have also computed quantum vibrational relaxation rates for both dimers in collision with a single (4)He and we find them to differ by orders of magnitude at the estimated surface temperature. Our results therefore confirm the findings from a great number of experimental data present in the current literature and provide one of the first attempts at giving an accurate, fully quantum picture for the nanoscopic properties of alkali dimers in (4)He clusters.

Structural analysis on mutation residues and interfacial water molecules for human TIM disease understanding

PubMed Central

2013-01-01

Background Human triosephosphate isomerase (HsTIM) deficiency is a genetic disease caused often by the pathogenic mutation E104D. This mutation, located at the side of an abnormally large cluster of water in the inter-subunit interface, reduces the thermostability of the enzyme. Why and how these water molecules are directly related to the excessive thermolability of the mutant have not been investigated in structural biology. Results This work compares the structure of the E104D mutant with its wild type counterparts. It is found that the water topology in the dimer interface of HsTIM is atypical, having a "wet-core-dry-rim" distribution with 16 water molecules tightly packed in a small deep region surrounded by 22 residues including GLU104. These water molecules are co-conserved with their surrounding residues in non-archaeal TIMs (dimers) but not conserved across archaeal TIMs (tetramers), indicating their importance in preserving the overall quaternary structure. As the structural permutation induced by the mutation is not significant, we hypothesize that the excessive thermolability of the E104D mutant is attributed to the easy propagation of atoms' flexibility from the surface into the core via the large cluster of water. It is indeed found that the B factor increment in the wet region is higher than other regions, and, more importantly, the B factor increment in the wet region is maintained in the deeply buried core. Molecular dynamics simulations revealed that for the mutant structure at normal temperature, a clear increase of the root-mean-square deviation is observed for the wet region contacting with the large cluster of interfacial water. Such increase is not observed for other interfacial regions or the whole protein. This clearly suggests that, in the E104D mutant, the large water cluster is responsible for the subunit interface flexibility and overall thermolability, and it ultimately leads to the deficiency of this enzyme. Conclusions Our study reveals that a large cluster of water buried in protein interfaces is fragile and high-maintenance, closely related to the structure, function and evolution of the whole protein. PMID:24564410

Formation, dissolution and properties of surface nanobubbles.

PubMed

Che, Zhizhao; Theodorakis, Panagiotis E

2017-02-01

Surface nanobubbles are stable gaseous phases in liquids that form on solid substrates. While their existence has been confirmed, there are many open questions related to their formation and dissolution processes along with their structures and properties, which are difficult to investigate experimentally. To address these issues, we carried out molecular dynamics simulations based on atomistic force fields for systems comprised of water, air (N 2 and O 2 ), and a Highly Oriented Pyrolytic Graphite (HOPG) substrate. Our results provide insights into the formation/dissolution mechanisms of nanobubbles and estimates for their density, contact angle, and surface tension. We found that the formation of nanobubbles is driven by an initial nucleation process of air molecules and the subsequent coalescence of the formed air clusters. The clusters form favorably on the substrate, which provides an enhanced stability to the clusters. In contrast, nanobubbles formed in the bulk either move randomly to the substrate and spread or move to the water-air surface and pop immediately. Moreover, nanobubbles consist of a condensed gaseous phase with a surface tension smaller than that of an equivalent system under atmospheric conditions, and contact angles larger than those in the equivalent nanodroplet case. We anticipate that this study will provide useful insights into the physics of nanobubbles and will stimulate further research in the field by using all-atom simulations. Copyright © 2016 Elsevier Inc. All rights reserved.

HF in clusters of molecular hydrogen. I. Size evolution of quantum solvation by parahydrogen molecules.

PubMed

Jiang, Hao; Bacić, Zlatko

2005-06-22

We present a theoretical study of the quantum solvation of the HF molecule by a small number of parahydrogen molecules, having n = 1-13 solvent particles. The minimum-energy cluster structures determined for n = 1-12 have all of the H(2) molecules in the first solvent shell. The first solvent shell closes at n = 12 and its geometry is icosahedral, with the HF molecule at the center. The quantum-mechanical ground-state properties of the clusters are calculated exactly using the diffusion Monte Carlo method. The zero-point energy of (p-H(2))(n)HF clusters is unusually large, amounting to 86% of the potential well depth for n > 7. The radial probability distribution functions (PDFs) confirm that the first solvent shell is complete for n = 12, and that the 13th p-H(2) molecule begins to fill the second solvent shell. The p-H(2) molecules execute large-amplitude motions and are highly mobile, making the solvent cage exceptionally fluxional. The anisotropy of the solvent, very pronounced for small clusters, decreases rapidly with increasing n, so that for n approximately 8-9 the solvent environment is practically isotropic. The analysis of the pair angular PDF reveals that for a given n, the parahydrogen solvent density around the HF is modulated in a pattern which clearly reflects the lowest-energy cluster configuration. The rigidity of the solvent clusters displays an interesting size dependence, increasing from n = 6 to 9, becoming floppier for n = 10, and increasing again up to n = 12, as the solvent shell is filled. The rigidity of the solvent cage appears to reach its maximum for n = 12, the point at which the first solvent shell is closed.

Microsolvation of Cl anion by water clusters: Pertubative Monte Carlo simulations using a hybrid HF/MM potential

NASA Astrophysics Data System (ADS)

Truong, Thanh N.; Stefanovich, Eugene V.

1997-05-01

We present a study of micro-solvation of Cl anion by water clusters of the size up to seven molecules using a perturbative Monte Carlo approach with a hybrid HF/MM potential. In this approach, a perturbation theory was used to avoid performing full SCF calculations at every Monte Carlo step. In this study, the anion is treated quantum mechanically at the HF/6-31G ∗ level of theory while interactions between solvent waters are presented by the TIP3P potential force field. Analysis on the solvent induced dipole moment of the ion indicates that the Cl anion resides most of the time on the surface of the clusters. Accuracy of the perturbative MC approach is also discussed.

Structural requirements and reaction pathways in dimethyl ether combustion catalyzed by supported Pt clusters.

PubMed

Ishikawa, Akio; Neurock, Matthew; Iglesia, Enrique

2007-10-31

The identity and reversibility of the elementary steps required for catalytic combustion of dimethyl ether (DME) on Pt clusters were determined by combining isotopic and kinetic analyses with density functional theory estimates of reaction energies and activation barriers to probe the lowest energy paths. Reaction rates are limited by C-H bond activation in DME molecules adsorbed on surfaces of Pt clusters containing chemisorbed oxygen atoms at near-saturation coverages. Reaction energies and activation barriers for C-H bond activation in DME to form methoxymethyl and hydroxyl surface intermediates show that this step is more favorable than the activation of C-O bonds to form two methoxides, consistent with measured rates and kinetic isotope effects. This kinetic preference is driven by the greater stability of the CH3OCH2* and OH* intermediates relative to chemisorbed methoxides. Experimental activation barriers on Pt clusters agree with density functional theory (DFT)-derived barriers on oxygen-covered Pt(111). Measured DME turnover rates increased with increasing DME pressure, but decreased as the O2 pressure increased, because vacancies (*) on Pt surfaces nearly saturated with chemisorbed oxygen are required for DME chemisorption. DFT calculations show that although these surface vacancies are required, higher oxygen coverages lead to lower C-H activation barriers, because the basicity of oxygen adatoms increases with coverage and they become more effective in hydrogen abstraction from DME. Water inhibits reaction rates via quasi-equilibrated adsorption on vacancy sites, consistent with DFT results indicating that water binds more strongly than DME on vacancies. These conclusions are consistent with the measured kinetic response of combustion rates to DME, O2, and H2O, with H/D kinetic isotope effects, and with the absence of isotopic scrambling in reactants containing isotopic mixtures of 18O2-16O2 or 12CH3O12CH3-13CH3O13CH3. Turnover rates increased with Pt cluster size, because small clusters, with more coordinatively unsaturated surface atoms, bind oxygen atoms more strongly than larger clusters and exhibit lower steady-state vacancy concentrations and a consequently smaller number of adsorbed DME intermediates involved in kinetically relevant steps. These effects of cluster size and metal-oxygen bond energies on reactivity are ubiquitous in oxidation reactions requiring vacancies on surfaces nearly saturated with intermediates derived from O2.

Expressed Glycosylphosphatidylinositol-Anchored Horseradish Peroxidase Identifies Co-Clustering Molecules in Individual Lipid Raft Domains

PubMed Central

Miyagawa-Yamaguchi, Arisa; Kotani, Norihiro; Honke, Koichi

2014-01-01

Lipid rafts that are enriched in glycosylphosphatidylinositol (GPI)-anchored proteins serve as a platform for important biological events. To elucidate the molecular mechanisms of these events, identification of co-clustering molecules in individual raft domains is required. Here we describe an approach to this issue using the recently developed method termed enzyme-mediated activation of radical source (EMARS), by which molecules in the vicinity within 300 nm from horseradish peroxidase (HRP) set on the probed molecule are labeled. GPI-anchored HRP fusion proteins (HRP-GPIs), in which the GPI attachment signals derived from human decay accelerating factor and Thy-1 were separately connected to the C-terminus of HRP, were expressed in HeLa S3 cells, and the EMARS reaction was catalyzed by these expressed HRP-GPIs under a living condition. As a result, these different HRP-GPIs had differences in glycosylation and localization and formed distinct clusters. This novel approach distinguished molecular clusters associated with individual GPI-anchored proteins, suggesting that it can identify co-clustering molecules in individual raft domains. PMID:24671047

Interaction of Gas Phase Oxalic Acid with Ammonia and its Atmospheric Implications

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

Peng, Xiu-Qiu; Liu, Yi-Rong; Huang, Teng

Oxalic acid is believed to play an important role in the formation and growth of atmospheric organic aerosols. However, as a common organic acid, the understanding of the larger clusters formed by gas phase oxalic acid with multiple ammonia molecules is incomplete. In this work, the structural characteristics and thermodynamics of oxalic acid clusters with up to six ammonia molecules have been investigated at the PW91PW91/6-311++G(3df,3pd) level of theory. We found that oxalic acid forms relatively stable clusters with ammonia molecules, and that ionization events play a key role. The analyses of the thermodynamics and atmospheric relevance indicate that themore » heterodimer (H2C2O4)(NH3) shows an obvious relative concentration in the atmosphere, and thus likely participates in new particle formation. However, with increasing number of ammonia molecules, the concentration of clusters decreases gradually. Additionally, clusters of oxalic acid with ammonia molecules are predicted to form favorably in low temperature conditions and show high Rayleigh scattering intensities.« less

Lipase immobilization for catalytic applications obtained using fumed silica deposited with MAPLE technique

NASA Astrophysics Data System (ADS)

Bloisi, Francesco; Califano, Valeria; Perretta, Giuseppe; Nasti, Libera; Aronne, Antonio; Di Girolamo, Rocco; Auriemma, Finizia; De Rosa, Claudio; Vicari, Luciano R. M.

2016-06-01

Lipases are enzymes used for catalyzing reactions of acylglycerides in biodiesel production from lipids, where enzyme immobilization on a substrate is required. Silica nanoparticles in different morphologies and configurations are currently used in conjunction with biological molecules for drug delivery and catalysis applications, but up to date their use for triglycerides has been limited by the large size of long-chain lipid molecules. Matrix assisted pulsed laser evaporation (MAPLE), a laser deposition technique using a frozen solution/suspension as a target, is widely used for deposition of biomaterials and other delicate molecules. We have carried out a MAPLE deposition starting from a frozen mixture containing fumed silica and lipase in water. Deposition parameters were chosen in order to increase surface roughness and to promote the formation of complex structures. Both the target (a frozen thickened mixture of nanoparticles/catalyst in water) and the deposition configuration (a small target to substrate distance) are unusual and have been adopted in order to increase surface contact of catalyst and to facilitate access to long-chain molecules. The resulting innovative film morphology (fumed silica/lipase cluster level aggregation) and the lipase functionality (for catalytic biodiesel production) have been studied by FESEM, FTIR and transesterification tests.

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

PubMed

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.

A novel approach to the theory of homogeneous and heterogeneous nucleation.

PubMed

Ruckenstein, Eli; Berim, Gersh O; Narsimhan, Ganesan

2015-01-01

A new approach to the theory of nucleation, formulated relatively recently by Ruckenstein, Narsimhan, and Nowakowski (see Refs. [7-16]) and developed further by Ruckenstein and other colleagues, is presented. In contrast to the classical nucleation theory, which is based on calculating the free energy of formation of a cluster of the new phase as a function of its size on the basis of macroscopic thermodynamics, the proposed theory uses the kinetic theory of fluids to calculate the condensation (W(+)) and dissociation (W(-)) rates on and from the surface of the cluster, respectively. The dissociation rate of a monomer from a cluster is evaluated from the average time spent by a surface monomer in the potential well as obtained from the solution of the Fokker-Planck equation in the phase space of position and momentum for liquid-to-solid transition and the phase space of energy for vapor-to-liquid transition. The condensation rates are calculated using traditional expressions. The knowledge of those two rates allows one to calculate the size of the critical cluster from the equality W(+)=W(-) as well as the rate of nucleation. The developed microscopic approach allows one to avoid the controversial application of classical thermodynamics to the description of nuclei which contain a few molecules. The new theory was applied to a number of cases, such as the liquid-to-solid and vapor-to-liquid phase transitions, binary nucleation, heterogeneous nucleation, nucleation on soluble particles and protein folding. The theory predicts higher nucleation rates at high saturation ratios (small critical clusters) than the classical nucleation theory for both solid-to-liquid as well as vapor-to-liquid transitions. As expected, at low saturation ratios for which the size of the critical cluster is large, the results of the new theory are consistent with those of the classical one. The present approach was combined with the density functional theory to account for the density profile in the cluster. This approach was also applied to protein folding, viewed as the evolution of a cluster of native residues of spherical shape within a protein molecule, which could explain protein folding/unfolding and their dependence on temperature. Copyright © 2014 Elsevier B.V. All rights reserved.

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

PubMed

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.

Biosynthetic Genes for the Tetrodecamycin Antibiotics

PubMed Central

Gverzdys, Tomas

2016-01-01

ABSTRACT We recently described 13-deoxytetrodecamycin, a new member of the tetrodecamycin family of antibiotics. A defining feature of these molecules is the presence of a five-membered lactone called a tetronate ring. By sequencing the genome of a producer strain, Streptomyces sp. strain WAC04657, and searching for a gene previously implicated in tetronate ring formation, we identified the biosynthetic genes responsible for producing 13-deoxytetrodecamycin (the ted genes). Using the ted cluster in WAC04657 as a reference, we found related clusters in three other organisms: Streptomyces atroolivaceus ATCC 19725, Streptomyces globisporus NRRL B-2293, and Streptomyces sp. strain LaPpAH-202. Comparing the four clusters allowed us to identify the cluster boundaries. Genetic manipulation of the cluster confirmed the involvement of the ted genes in 13-deoxytetrodecamycin biosynthesis and revealed several additional molecules produced through the ted biosynthetic pathway, including tetrodecamycin, dihydrotetrodecamycin, and another, W5.9, a novel molecule. Comparison of the bioactivities of these four molecules suggests that they may act through the covalent modification of their target(s). IMPORTANCE The tetrodecamycins are a distinct subgroup of the tetronate family of secondary metabolites. Little is known about their biosynthesis or mechanisms of action, making them an attractive subject for investigation. In this paper we present the biosynthetic gene cluster for 13-deoxytetrodecamycin in Streptomyces sp. strain WAC04657. We identify related clusters in several other organisms and show that they produce related molecules. PMID:27137499

First principles investigations of small bimetallic PdGa clusters as catalysts for hydrogen dissociation

NASA Astrophysics Data System (ADS)

Kaul, Indu; Ghosh, Prasenjit

2017-04-01

Using first principles density functional theory based calculations, we have studied hydrogen dissociation on sub nanometer bimetallic clusters formed from d-block (Pd) and p-block (Ga) elements in gas phase to explore the feasibility of using them as cheap catalysts for hydrogen dissociation. Our calculations show that the dimers, trimers and tetramers of these clusters are thermodynamically more stable than the pure ones for all Ga concentrations. For a given cluster size, we find that the clusters containing equal amount of Pd and Ga are the most stable ones. In contrast to bulk PdGa, the contribution of Pd-d states to the highest occupied molecular orbitals of the bimetallic clusters are either very small or absent. Study of adsorption of hydrogen molecule on these clusters show that hydrogen binds in an activated form only on the Pd rich clusters. From the calculations of hydrogen dissociation barriers on tetramers of pure Pd, 25% Ga (Pd3Ga) and 50% Ga (Pd2Ga2) we find that Pd3Ga is the most efficient catalyst for hydrogen dissociation with barriers even lower than that on the PdGa surfaces.

Low energy isomers of (H2O)25 from a hierarchical method based on Monte Carlo Temperature Basin Paving and Molecular Tailoring Approaches benchmarked by full MP2 calculations

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

Sahu, Nityananda; Gadre, Shridhar R.; Bandyopadhyay, Pradipta

We report new global minimum candidate structures for the (H2O)25 cluster that are lower in energy than the ones reported previously and correspond to hydrogen bonded networks with 42 hydrogen bonds and an interior, fully coordinated water molecule. These were obtained as a result of a hierarchical approach based on initial Monte Carlo Temperature Basin Paving (MCTBP) sampling of the cluster’s Potential Energy Surface (PES) with the Effective Fragment Potential (EFP), subsequent geometry optimization using the Molecular Tailoring fragmentation Approach (MTA) and final refinement at the second order Møller Plesset perturbation (MP2) level of theory. The MTA geometry optimizations usedmore » between 14 and 18 main fragments with maximum sizes between 11 and 14 water molecules and average size of 10 water molecules, whose energies and gradients were computed at the MP2 level. The MTA-MP2 optimized geometries were found to be quite close (within < 0.5 kcal/mol) to the ones obtained from the MP2 optimization of the whole cluster. The grafting of the MTA-MP2 energies yields electronic energies that are within < 5×10-4 a.u. from the MP2 results for the whole cluster while preserving their energy order. The MTA-MP2 method was also found to reproduce the MP2 harmonic vibrational frequencies in both the HOH bending and the OH stretching regions.« less

Molecular Occupancy of Nanodot Arrays.

PubMed

Cai, Haogang; Wolfenson, Haguy; Depoil, David; Dustin, Michael L; Sheetz, Michael P; Wind, Shalom J

2016-04-26

Single-molecule nanodot arrays, in which a biomolecule of choice (protein, nucleic acid, etc.) is bound to a metallic nanoparticle on a solid substrate, are becoming an increasingly important tool in the study of biomolecular and cellular interactions. We have developed an on-chip measurement protocol to monitor and control the molecular occupancy of nanodots. Arrays of widely spaced nanodots and nanodot clusters were fabricated on glass surfaces by nanolithography and functionalized with fluorescently labeled proteins. The molecular occupancy was determined by monitoring individual fluorophore bleaching events, while accounting for fluorescence quenching effects. We found that the occupancy can be interpreted as a packing problem, and depends on nanodot size and binding ligand concentration, where the latter is easily adjusted to compensate the flexibility of dimension control in nanofabrication. The results are scalable with nanodot cluster size, extending to large area close packed arrays. As an example, the nanoarray platform was used to probe the geometric requirement of T-cell activation at the single-molecule level.

Measuring the internal energies of species emitted from hypervelocity nanoprojectile impacts on surfaces using recalibrated benzylpyridinium probe ions

NASA Astrophysics Data System (ADS)

DeBord, J. Daniel; Verkhoturov, Stanislav V.; Perez, Lisa M.; North, Simon W.; Hall, Michael B.; Schweikert, Emile A.

2013-06-01

We present herein a framework for measuring the internal energy distributions of vibrationally excited molecular ions emitted from hypervelocity nanoprojectile impacts on organic surfaces. The experimental portion of this framework is based on the measurement of lifetime distributions of "thermometer" benzylpyridinium ions dissociated within a time of flight mass spectrometer. The theoretical component comprises re-evaluation of the fragmentation energetics of benzylpyridinium ions at the coupled-cluster singles and doubles with perturbative triples level. Vibrational frequencies for the ground and transition states of select molecules are reported, allowing for a full description of vibrational excitations of these molecules via Rice-Ramsperger-Kassel-Marcus unimolecular fragmentation theory. Ultimately, this approach is used to evaluate the internal energy distributions from the measured lifetime distributions. The average internal energies of benzylpyridinium ions measured from 440 keV Au400+4 impacts are found to be relatively low (˜0.24 eV/atom) when compared with keV atomic bombardment of surfaces (1-2 eV/atom).

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

Marlow, W.H.

An aerosol here is understood to be a two-component system comprised of gaseous and condensed phases with the characteristic that the condensed phase is not an equilibrium subsystem. In contrast to the usual definitions based upon geometrical or mechanical variables, this quasi-thermodynamic formulation is framed to emphasize the dynamical behavior of aerosols by allowing for coagulation and other aerosol evolutionary processes as natural consequences of the interactions and state variables appropriate to the system. As will become clear later, it also provides a point of departure for distinguishing aerosol particles from unstable gas-phase cluster systems. The question of accommodation inmore » particle collisions must be addressed as a prelude to the discussion of the role of long-range forces. Microscopic reversibility is frequently assumed for molecular collisions with either molecules or solid surfaces. In the case of aerosol collisions, the implication of this assumption is that collisions are elastic, which is contrary to the evidence from coagulation experiments and the conventional operational assumption of sticking upon collision. Gay and Berne have performed computer simulations of the collision of two clusters consisting of a total of 135 molecules interacting via Lennard-Jones potentials. That work showed that complete accommodation, accompanied by overall heating of the unified cluster, occurred. Since heating represents an irreversible degradation of the kinetic energy of the collision, the hamiltonian of the two-cluster system should be considered as dissipative and therefore microscopic reversibility does not apply.« less

Analyzing ZnO clusters through the density-functional theory.

PubMed

Zaragoza, Irineo-Pedro; Soriano-Agueda, Luis-Antonio; Hernández-Esparza, Raymundo; Vargas, Rubicelia; Garza, Jorge

2018-06-16

The potential energy surface of Zn n O n clusters (n = 2, 4, 6, 8) has been explored by using a simulated annealing method. For n = 2, 4, and 6, the CCSD(T)/TZP method was used as the reference, and from here it is shown that the M06-2X/TZP method gives the lowest deviations over PBE, PBE0, B3LYP, M06, and MP2 methods. Thus, with the M06-2X method we predict isomers of Zn n O n clusters, which coincide with some isomers reported previously. By using the atoms in molecules analysis, possible contacts between Zn and O atoms were found for all structures studied in this article. The bond paths involved in several clusters suggest that Zn n O n clusters can be obtained from the zincite (ZnO crystal), such an observation was confirmed for clusters with n = 2 - 9,18 and 20. The structure with n = 23 was obtained by the procedure presented here, from crystal information, which could be important to confirm experimental data delivered for n = 18 and 23.

Electron-induced chemistry in microhydrated sulfuric acid clusters

NASA Astrophysics Data System (ADS)

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.

The Measurement of Sulfur Oxidation Products and Their Role in Homogeneous Nucleation

NASA Technical Reports Server (NTRS)

Eisele, F. L.

1999-01-01

An improved version of a transverse ion source was developed which uses selected ion chemical ionization mass spectrometry techniques inside of a particle nucleation flow tube. These new techniques are very unique, in that the chemical ionization is done inside of the flow tube rather than by having to remove the compounds and clusters of interest which are lost on first contact,with any surfaces. The transverse source is also unique because it allows the ion reaction time to be varied over more than an order of magnitude, which in turn makes possible the separation of ion induced cluster growth from the charging of preexisting molecular clusters. As a result of combining these unique capabilities, the first ever measurements of prenucleation molecular clusters were performed. These clusters are the intermediate stage of growth in the gas-to-particle conversion process. This new technique provides a means of observing clusters containing 2, 3, 4, ... and up to about 8 sulfuric acid molecules, where the critical cluster size under these measurement conditions was about 4 or 5. Thus, the nucleation process can now be directly observed and even growth beyond the critical cluster size can be investigated. The details of this investigation are discussed in a recently submitted paper, which is included as Appendix A. Measurements of the diffusion coefficient of sulfuric acid and sulfuric acid clustered with a water molecule have also been performed. The measurements are also discussed in more detail in another recently submitted paper which is included as Appendix B. The empirical results discussed in both of these papers provide a critical test of present nucleation theories. They also provide new hope for resolving many of the huge discrepancies between field observation and model prediction of particle nucleation. The second part of the research conducted under this project was directed towards the development of new chemical ionization techniques for measuring sulfur oxidation products.

Study of lithium cation in water clusters: based on atom-bond electronegativity equalization method fused into molecular mechanics.

PubMed

Li, Xin; Yang, Zhong-Zhi

2005-05-12

We present a potential model for Li(+)-water clusters based on a combination of the atom-bond electronegativity equalization and molecular mechanics (ABEEM/MM) that is to take ABEEM charges of the cation and all atoms, bonds, and lone pairs of water molecules into the intermolecular electrostatic interaction term in molecular mechanics. The model allows point charges on cationic site and seven sites of an ABEEM-7P water molecule to fluctuate responding to the cluster geometry. The water molecules in the first sphere of Li(+) are strongly structured and there is obvious charge transfer between the cation and the water molecules; therefore, the charge constraint on the ionic cluster includes the charged constraint on the Li(+) and the first-shell water molecules and the charge neutrality constraint on each water molecule in the external hydration shells. The newly constructed potential model based on ABEEM/MM is first applied to ionic clusters and reproduces gas-phase state properties of Li(+)(H(2)O)(n) (n = 1-6 and 8) including optimized geometries, ABEEM charges, binding energies, frequencies, and so on, which are in fair agreement with those measured by available experiments and calculated by ab initio methods. Prospects and benefits introduced by this potential model are pointed out.

Detection of nerve gases using surface-enhanced Raman scattering substrates with high droplet adhesion

NASA Astrophysics Data System (ADS)

Hakonen, Aron; Rindzevicius, Tomas; Schmidt, Michael Stenbæk; Andersson, Per Ola; Juhlin, Lars; Svedendahl, Mikael; Boisen, Anja; Käll, Mikael

2016-01-01

Threats from chemical warfare agents, commonly known as nerve gases, constitute a serious security issue of increasing global concern because of surging terrorist activity worldwide. However, nerve gases are difficult to detect using current analytical tools and outside dedicated laboratories. Here we demonstrate that surface-enhanced Raman scattering (SERS) can be used for sensitive detection of femtomol quantities of two nerve gases, VX and Tabun, using a handheld Raman device and SERS substrates consisting of flexible gold-covered Si nanopillars. The substrate surface exhibits high droplet adhesion and nanopillar clustering due to elasto-capillary forces, resulting in enrichment of target molecules in plasmonic hot-spots with high Raman enhancement. The results may pave the way for strategic life-saving SERS detection of chemical warfare agents in the field.Threats from chemical warfare agents, commonly known as nerve gases, constitute a serious security issue of increasing global concern because of surging terrorist activity worldwide. However, nerve gases are difficult to detect using current analytical tools and outside dedicated laboratories. Here we demonstrate that surface-enhanced Raman scattering (SERS) can be used for sensitive detection of femtomol quantities of two nerve gases, VX and Tabun, using a handheld Raman device and SERS substrates consisting of flexible gold-covered Si nanopillars. The substrate surface exhibits high droplet adhesion and nanopillar clustering due to elasto-capillary forces, resulting in enrichment of target molecules in plasmonic hot-spots with high Raman enhancement. The results may pave the way for strategic life-saving SERS detection of chemical warfare agents in the field. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr06524k

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

PubMed

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- < Naph- < Anth- < Py-DTC. This shift is reversible upon removal of Py-DTC by triethylphosphine gold(i) chloride treatment at room temperature. Furthermore, we performed temperature-dependent (80-300 K) photoluminescence lifetime measurements, which show longer lifetime at lower temperature, suggesting a strong influence of hole 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.

Nature of bonding and cooperativity in linear DMSO clusters: A DFT, AIM and NCI analysis.

PubMed

Venkataramanan, Natarajan Sathiyamoorthy; Suvitha, Ambigapathy

2018-05-01

This study aims to cast light on the nature of interactions and cooperativity that exists in linear dimethyl sulfoxide (DMSO) clusters using dispersion corrected density functional theory. In the linear DMSO, DMSO molecules in the middle of the clusters are bound strongly than at the terminal. The plot of the total binding energy of the clusters vs the cluster size and mean polarizabilities vs cluster size shows an excellent linearity demonstrating the presence of cooperativity effect. The computed incremental binding energy of the clusters remains nearly constant, implying that DMSO addition at the terminal site can happen to form an infinite chain. In the linear clusters, two σ-hole at the terminal DMSO molecules were found and the value on it was found to increase with the increase in cluster size. The quantum theory of atoms in molecules topography shows the existence of hydrogen and SO⋯S type in linear tetramer and larger clusters. In the dimer and trimer SO⋯OS type of interaction exists. In 2D non-covalent interactions plot, additional peaks in the regions which contribute to the stabilization of the clusters were observed and it splits in the trimer and intensifies in the larger clusters. In the trimer and larger clusters in addition to the blue patches due to hydrogen bonds, additional, light blue patches were seen between the hydrogen atom of the methyl groups and the sulphur atom of the nearby DMSO molecule. Thus, in addition to the strong H-bonds, strong electrostatic interactions between the sulphur atom and methyl hydrogens exists in the linear clusters. Copyright © 2018 Elsevier Inc. All rights reserved.

DNA-templated synthesis of Pt nanoparticles on single-walled carbon nanotubes.

PubMed

Dong, Lifeng

2009-11-18

A series of electron microscopy characterizations demonstrate that single-stranded deoxyribonucleic acid (ssDNA) can bind to nanotube surfaces and disperse bundled single-walled carbon nanotubes (SWCNTs) into individual tubes. The ssDNA molecules on the nanotube surfaces demonstrate various morphologies, such as aggregated clusters and spiral wrapping around a nanotube with different pitches and spaces, indicating that the morphology of the SWCNT/DNA hybrids is not related solely to the base sequence of the ssDNA or the chirality or the diameter of the nanotubes. In addition to serving as a non-covalent dispersion agent, the ssDNA molecules bonded to the nanotube surface can provide addresses for localizing Pt(II) complexes along the nanotubes. The Pt nanoparticles obtained by a reduction of the Pt2+-DNA adducts are crystals with a size of < or =1-2 nm. These results expand our understanding of the interactions between ssDNA and SWCNTs and provide an efficient approach for positioning Pt and other metal particles, with uniform sizes and without aggregations, along the nanotube surfaces for applications in direct ethanol/methanol fuel cells and nanoscale electronics.

Rotational spectroscopic study of carbonyl sulfide solvated with hydrogen molecules.

PubMed

Michaud, Julie M; Jäger, Wolfgang

2008-10-14

Rotational spectra of small-sized (H(2))(N)-OCS clusters with N = 2-7 were measured using a pulsed-jet Fourier transform microwave spectrometer. These include spectra of pure (para-H(2))(N)-OCS clusters, pure (ortho-H(2))(N)-OCS clusters, and mixed ortho-H(2) and para-H(2) containing clusters. The rotational lines of ortho-H(2) molecules containing clusters show proton spin-proton spin hyperfine structure, and the pattern evolves as the number of ortho-H(2) molecules in the cluster increases. Various isotopologues of the clusters were investigated, including those with O(13)CS, OC(33)S, OC(34)S, and O(13)C(34)S. Nuclear quadrupole hyperfine structures of rotational transitions were observed for (33)S (nuclear spin quantum number I = 3/2) containing isotopologues. The (33)S nuclear quadrupole coupling constants are compared to the corresponding constant of the OCS monomer and those of the He(N)-OCS clusters. The assignment of the number of solvating hydrogen molecules N is supported by the analyses of the proton spin-proton spin hyperfine structures of the mixed clusters, the dependence of line intensities on sample conditions (pressure and concentrations), and the agreement of the (para-H(2))(N)-OCS and (ortho-H(2))(N)-OCS rotational constants with those from a previous infrared study [J. Tang and A. R. W. McKellar, J. Chem. Phys. 121, 3087 (2004)].

Free-surface microfluidics for detection of airborne explosives

NASA Astrophysics Data System (ADS)

Meinhart, Carl; Piorek, Brian; Banerjee, Sanjoy; Lee, Seung Joon; Moskovits, Martin

2008-11-01

A novel microfluidic, remote-sensing, chemical detection platform has been developed for real-time sensing of airborne agents. The key enabling technology is a newly developed concept termed Free-Surface Fluidics (FSF), where one or more fluidic surfaces of a microchannel flow are confined by surface tension and exposed to the surrounding atmosphere. The result is a unique open channel flow environment that is driven by pressure through surface tension, and not subject to body forces, such as gravity. Evaporation and flow rates are controlled by microchannel geometry, surface chemistry and precisely-controlled temperature profiles. The free-surface fluidic architecture is combined with Surface-Enhanced Raman Spectroscopy (SERS) to allow for real-time profiling of atmospheric species and detection of airborne agents. The aggregation of SERS nanoparticles is controlled using microfluidics, to obtain dimer nanoparticle clusters at known streamwise positions in the microchannel. These dimers form SERS hot-spots, which amplify the Raman signal by 8 -- 10 orders of magnitude. Results indicate that explosive agents such as DNT, TNT, RDX, TATP and picric acid in the surrounding atmosphere can be readily detected by the SERS system. Due to the amplification of the SERS system, explosive molecules with concentrations of parts per trillion can be detected, even in the presence of interferent molecules having six orders of magnitude higher concentration.

Surface anisotropy of iron oxide nanoparticles and slabs from first principles: Influence of coatings and ligands as a test of the Heisenberg model

NASA Astrophysics Data System (ADS)

Brymora, Katarzyna; Calvayrac, Florent

2017-07-01

We performed ab initio computations of the magnetic properties of simple iron oxide clusters and slabs. We considered an iron oxide cluster functionalized by a molecule or glued to a gold cluster of the same size. We also considered a magnetite slab coated by cobalt oxide or a mixture of iron oxide and cobalt oxide. The changes in magnetic behavior were explored using constrained magnetic calculations. A possible value for the surface anisotropy was estimated from the fit of a classical Heisenberg model on ab initio results. The value was found to be compatible with estimations obtained by other means, or inferred from experimental results. The addition of a ligand, coating, or of a metallic nanoparticle to the systems degraded the quality of the description by the Heisenberg Hamiltonian. Proposing a change in the anisotropies allowing for the proportion of each transition atom we could get a much better description of the magnetism of series of hybrid cobalt and iron oxide systems.

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

NASA Astrophysics Data System (ADS)

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.

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

PubMed

Pohl, Gábor; Mones, Letif; Turi, László

2016-10-28

We performed a series of comparative quantum chemical calculations on various size negatively charged methanol clusters, 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.

Tungsten Hydride Phosphorus- and Arsenic-Bearing Molecules with Double and Triple W-P and W-As Bonds.

PubMed

Andrews, Lester; Cho, Han-Gook; Fang, Zongtang; Vasiliu, Monica; Dixon, David A

2018-05-07

Laser ablation of tungsten metal provides W atoms which react with phosphine and arsine during condensation in excess argon and neon, leading to major new infrared (IR) absorptions. Annealing, UV irradiation, and deuterium substitution experiments coupled with electronic structure calculations at the density functional theory level led to the assignment of the observed IR absorptions to the E≡WH 3 and HE═WH 2 molecules for E = P and As. The potential energy surfaces for hydrogen transfer from PH 3 to the W were calculated at the coupled-cluster CCSD(T)/complete basis set level. Additional weak bands in the phosphide and arsenide W-H stretching region are assigned to the molecules with loss of H from W, E≡WH 2 . The electronic structure calculations show that the E≡WH 3 molecules have a W-E triple bond, the HE═WH 2 molecules have a W-E double bond, and the H 2 E-WH molecules have a W-E single bond. The formation of multiple E-W bonds leads to increasing stability for the isomers.

Aggregation Number in Water/n-Hexanol Molecular Clusters Formed in Cyclohexane at Different Water/n-Hexanol/Cyclohexane Compositions Calculated by Titration 1H NMR.

PubMed

Flores, Mario E; Shibue, Toshimichi; Sugimura, Natsuhiko; Nishide, Hiroyuki; Moreno-Villoslada, Ignacio

2017-11-09

Upon titration of n-hexanol/cyclohexane mixtures of different molar compositions with water, water/n-hexanol clusters are formed in cyclohexane. Here, we develop a new method to estimate the water and n-hexanol aggregation numbers in the clusters that combines integration analysis in one-dimensional 1 H NMR spectra, diffusion coefficients calculated by diffusion-ordered NMR spectroscopy, and further application of the Stokes-Einstein equation to calculate the hydrodynamic volume of the clusters. Aggregation numbers of 5-15 molecules of n-hexanol per cluster in the absence of water were observed in the whole range of n-hexanol/cyclohexane molar fractions studied. After saturation with water, aggregation numbers of 6-13 n-hexanol and 0.5-5 water molecules per cluster were found. O-H and O-O atom distances related to hydrogen bonds between donor/acceptor molecules were theoretically calculated using density functional theory. The results show that at low n-hexanol molar fractions, where a robust hydrogen-bond network is held between n-hexanol molecules, addition of water makes the intermolecular O-O atom distance shorter, reinforcing molecular association in the clusters, whereas at high n-hexanol molar fractions, where dipole-dipole interactions dominate, addition of water makes the intermolecular O-O atom distance longer, weakening the cluster structure. This correlates with experimental NMR results, which show an increase in the size and aggregation number in the clusters upon addition of water at low n-hexanol molar fractions, and a decrease of these magnitudes at high n-hexanol molar fractions. In addition, water produces an increase in the proton exchange rate between donor/acceptor molecules at all n-hexanol molar fractions.

A quantitative study of the clustering of polycyclic aromatic hydrocarbons at high temperatures.

PubMed

Totton, Tim S; Misquitta, Alston J; Kraft, Markus

2012-03-28

The clustering of polycyclic aromatic hydrocarbon (PAH) molecules is investigated in the context of soot particle inception and growth using an isotropic potential developed from the benchmark PAHAP potential. This potential is used to estimate equilibrium constants of dimerisation for five representative PAH molecules based on a statistical mechanics model. Molecular dynamics simulations are also performed to study the clustering of homomolecular systems at a range of temperatures. The results from both sets of calculations demonstrate that at flame temperatures pyrene (C(16)H(10)) dimerisation cannot be a key step in soot particle formation and that much larger molecules (e.g. circumcoronene, C(54)H(18)) are required to form small clusters at flame temperatures. The importance of using accurate descriptions of the intermolecular interactions is demonstrated by comparing results to those calculated with a popular literature potential with an order of magnitude variation in the level of clustering observed. By using an accurate intermolecular potential we are able to show that physical binding of PAH molecules based on van der Waals interactions alone can only be a viable soot inception mechanism if concentrations of large PAH molecules are significantly higher than currently thought.

Dynamics of Surfactant Clustering at Interfaces and Its Influence on the Interfacial Tension: Atomistic Simulation of a Sodium Hexadecane-Benzene Sulfonate-Tetradecane-Water System.

PubMed

Paredes, Ricardo; Fariñas-Sánchez, Ana Isabel; Medina-Rodrı Guez, Bryan; Samaniego, Samantha; Aray, Yosslen; Álvarez, Luis Javier

2018-03-06

The process of equilibration of the tetradecane-water interface in the presence of sodium hexadecane-benzene sulfonate is studied using intensive atomistic molecular dynamics simulations. Starting as an initial point with all of the surfactants at the interface, it is obtained that the equilibration time of the interface (several microseconds) is orders of magnitude higher than previously reported simulated times. There is strong evidence that this slow equilibration process is due to the aggregation of surfactants molecules on the interface. To determine this fact, temporal evolution of interfacial tension and interfacial formation energy are studied and their temporal variations are correlated with cluster formation. To study cluster evolution, the mean cluster size and the probability that a molecule of surfactant chosen at random is free are obtained as a function of time. Cluster size distribution is estimated, and it is observed that some of the molecules remain free, whereas the rest agglomerate. Additionally, the temporal evolution of the interfacial thickness and the structure of the surfactant molecules on the interface are studied. It is observed how this structure depends on whether the molecules agglomerate or not.

Structure of a premicellar complex of alkyl sulfates with the interfacial binding surfaces of four subunits of phospholipase A2.

PubMed

Pan, Ying H; Bahnson, Brian J

2010-07-01

The properties of three discrete premicellar complexes (E1#, E2#, E3#) of pig pancreatic group-IB secreted phospholipase A2 (sPLA2) with monodisperse alkyl sulfates have been characterized [Berg, O. G. et al., Biochemistry 43, 7999-8013, 2004]. Here we have solved the 2.7 A crystal structure of group-IB sPLA2 complexed with 12 molecules of octyl sulfate (C8S) in a form consistent with a tetrameric oligomeric that exists during the E1# phase of premicellar complexes. The alkyl tails of the C8S molecules are centered in the middle of the tetrameric cluster of sPLA2 subunits. Three of the four sPLA2 subunits also contain a C8S molecule in the active site pocket. The sulfate oxygen of a C8S ligand is complexed to the active site calcium in three of the four protein active sites. The interactions of the alkyl sulfate head group with Arg-6 and Lys-10, as well as the backbone amide of Met-20, are analogous to those observed in the previously solved sPLA2 crystal structures with bound phosphate and sulfate anions. The cluster of three anions found in the present structure is postulated to be the site for nucleating the binding of anionic amphiphiles to the interfacial surface of the protein, and therefore this binding interaction has implications for interfacial activation of the enzyme. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Polycyclic aromatic hydrocarbons in model bacterial membranes - Langmuir monolayer studies.

PubMed

Broniatowski, Marcin; Binczycka, Martyna; Wójcik, Aneta; Flasiński, Michał; Wydro, Paweł

2017-12-01

High molecular weight polycyclic aromatic hydrocarbons (HMW-PAHs) are persistent organic pollutants which due to their limited biodegradability accumulate in soils where their increased presence can lead to the impoverishment of the decomposer organisms. As very hydrophobic PAHs easily penetrate cellular membranes of soil bacteria and can be incorporated therein, changing the membrane fluidity and other functions which in consequence can lead to the death of the organism. The structure and size of PAH molecule can be crucial for its membrane activity; however the correlation between PAH structure and its interaction with phospholipids have not been investigated so far. In our studies we applied phospholipid Langmuir monolayers as model bacterial membranes and investigated how the incorporation of six structurally different PAH molecules change the membrane texture and physical properties. In our studies we registered surface pressure and surface potential isotherms upon the monolayer compression, visualized the monolayer texture with the application of Brewster angle microscopy and searched the ordering of the film-forming molecules with molecular resolution with the application of grazing incidence X-ray diffraction (GIXD) method. It turned out that the phospholipid-PAH interactions are strictly structure dependent. Four and five-ring PAHs of the angular or cluster geometry can be incorporated into the model membranes changing profoundly their textures and fluidity; whereas linear or large cluster PAHs cannot be incorporated and separate from the lipid matrix. The observed phenomena were explained based on structural similarities of the applied PAHs with membrane steroids and hopanoids. Copyright © 2017. Published by Elsevier B.V.

Interactions between glycine and amorphous solid water nanoscale films

NASA Astrophysics Data System (ADS)

Tzvetkov, George; Koller, Georg; Netzer, Falko P.

2012-12-01

The interactions of glycine (Gly) with amorphous solid water (ASW) nanolayers (≤ 100 ML), vapor-deposited on single crystalline AlOx surfaces at 100 K, have been investigated by near-edge X-ray absorption fine structure spectroscopy (NEXAFS) at the oxygen K-edge, temperature-programmed thermal desorption (TPD), X-ray photoelectron spectroscopy (XPS), and temperature-dependent work function measurements. Gly-on-ASW, ASW-on-Gly, and Gly on top of ASW-on-Gly ultrathin films have been fabricated. In contrast to the uniform ASW films grown directly on the hydrophilic AlOx, water molecules adsorb on the hydrophobic Gly films in the form of 3D ASW clusters. This leads to significant differences in the NEXAFS and work function data obtained from ASW-on-AlOx and ASW-on-Gly films, respectively. Furthermore, these structural differences influence the chemical state of Gly molecules (neutral vs. zwitterionic) adsorbed on top of ASW films. N1s XPS measurements revealed an increased amount of neutral Gly molecules in the film top-deposited on the ASW-on-Gly structure in comparison to the neutral Gly in the films directly condensed on AlOx or grown on the ASW substrate. H2O TPD spectra demonstrate that the crystallization and desorption processes of ASW are affected in a different way by the Gly layers, top-deposited on to ASW-on-AlOx and ASW-on-Gly films. At the same time, Gly adlayers sink into the ASW film during crystallization/desorption of the latter and land softly on the alumina surface in the form of zwitterionic clusters.

Structures, electronic properties and reaction paths from Fe(CO)5 molecule to small Fe clusters

NASA Astrophysics Data System (ADS)

Li, Zhi; Zhao, Zhen

2018-04-01

The geometries, electrical characters and reaction paths from Fe(CO)5 molecule to small Fe clusters were investigated by using all-electron density functional theory. The results show that in the decomposition process of pentacarbonyl-iron, Fe(CO)5 molecule prefers to remove a carbon monoxide and adsorb another Fe(CO)5 molecule to produce nonacarbonyldiiron Fe2(CO)9 then Fe2(CO)9 gradually removes carbon monoxide to produce small Fe clusters. As It can be seen from the highest occupied molecule orbital-lowest unoccupied molecule orbital gap curves, the Fe(CO)n=3, and 5 and Fe2(CO)n=3, 7 and 9 intermediates have higher chemical stability than their neighbors. The local magnetic moment of the carbon monoxide is aligning anti-ferromagnetic. The effect of external magnetic field to the initial decomposition products of Fe(CO)5 can be ignored.

Biosynthetic Genes for the Tetrodecamycin Antibiotics.

PubMed

Gverzdys, Tomas; Nodwell, Justin R

2016-07-15

We recently described 13-deoxytetrodecamycin, a new member of the tetrodecamycin family of antibiotics. A defining feature of these molecules is the presence of a five-membered lactone called a tetronate ring. By sequencing the genome of a producer strain, Streptomyces sp. strain WAC04657, and searching for a gene previously implicated in tetronate ring formation, we identified the biosynthetic genes responsible for producing 13-deoxytetrodecamycin (the ted genes). Using the ted cluster in WAC04657 as a reference, we found related clusters in three other organisms: Streptomyces atroolivaceus ATCC 19725, Streptomyces globisporus NRRL B-2293, and Streptomyces sp. strain LaPpAH-202. Comparing the four clusters allowed us to identify the cluster boundaries. Genetic manipulation of the cluster confirmed the involvement of the ted genes in 13-deoxytetrodecamycin biosynthesis and revealed several additional molecules produced through the ted biosynthetic pathway, including tetrodecamycin, dihydrotetrodecamycin, and another, W5.9, a novel molecule. Comparison of the bioactivities of these four molecules suggests that they may act through the covalent modification of their target(s). The tetrodecamycins are a distinct subgroup of the tetronate family of secondary metabolites. Little is known about their biosynthesis or mechanisms of action, making them an attractive subject for investigation. In this paper we present the biosynthetic gene cluster for 13-deoxytetrodecamycin in Streptomyces sp. strain WAC04657. We identify related clusters in several other organisms and show that they produce related molecules. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Positive feedback can lead to dynamic nanometer-scale clustering on cell membranes

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

Wehrens, Martijn; Rein ten Wolde, Pieter; Mugler, Andrew, E-mail: amugler@purdue.edu

2014-11-28

Clustering of molecules on biological membranes is a widely observed phenomenon. A key example is the clustering of the oncoprotein Ras, which is known to be important for signal transduction in mammalian cells. Yet, the mechanism by which Ras clusters form and are maintained remains unclear. Recently, it has been discovered that activated Ras promotes further Ras activation. Here we show using particle-based simulation that this positive feedback is sufficient to produce persistent clusters of active Ras molecules at the nanometer scale via a dynamic nucleation mechanism. Furthermore, we find that our cluster statistics are consistent with experimental observations ofmore » the Ras system. Interestingly, we show that our model does not support a Turing regime of macroscopic reaction-diffusion patterning, and therefore that the clustering we observe is a purely stochastic effect, arising from the coupling of positive feedback with the discrete nature of individual molecules. These results underscore the importance of stochastic and dynamic properties of reaction diffusion systems for biological behavior.« less

Surface passivation for tight-binding calculations of covalent solids.

PubMed

Bernstein, N

2007-07-04

Simulation of a cluster representing a finite portion of a larger covalently bonded system requires the passivation of the cluster surface. We compute the effects of an explicit hybrid orbital passivation (EHOP) on the atomic structure in a model bulk, three-dimensional, narrow gap semiconductor, which is very different from the wide gap, quasi-one-dimensional organic molecules where most passivation schemes have been studied in detail. The EHOP approach is directly applicable to minimal atomic orbital basis methods such as tight-binding. Each broken bond is passivated by a hybrid created from an explicitly expressed linear combination of basis orbitals, chosen to represent the contribution of the missing neighbour, e.g. a sp(3) hybrid for a single bond. The method is tested by computing the forces on atoms near a point defect as a function of cluster geometry. We show that, compared to alternatives such as pseudo-hydrogen passivation, the force on an atom converges to the correct bulk limit more quickly as a function of cluster radius, and that the force is more stable with respect to perturbations in the position of the cluster centre. The EHOP method also obviates the need for parameterizing the interactions between the system atoms and the passivating atoms. The method is useful for cluster calculations of non-periodic defects in large systems and for hybrid schemes that simulate large systems by treating finite regions with a quantum-mechanical model, coupled to an interatomic potential description of the rest of the system.

Surface passivation for tight-binding calculations of covalent solids

NASA Astrophysics Data System (ADS)

Bernstein, N.

2007-07-01

Simulation of a cluster representing a finite portion of a larger covalently bonded system requires the passivation of the cluster surface. We compute the effects of an explicit hybrid orbital passivation (EHOP) on the atomic structure in a model bulk, three-dimensional, narrow gap semiconductor, which is very different from the wide gap, quasi-one-dimensional organic molecules where most passivation schemes have been studied in detail. The EHOP approach is directly applicable to minimal atomic orbital basis methods such as tight-binding. Each broken bond is passivated by a hybrid created from an explicitly expressed linear combination of basis orbitals, chosen to represent the contribution of the missing neighbour, e.g. a sp3 hybrid for a single bond. The method is tested by computing the forces on atoms near a point defect as a function of cluster geometry. We show that, compared to alternatives such as pseudo-hydrogen passivation, the force on an atom converges to the correct bulk limit more quickly as a function of cluster radius, and that the force is more stable with respect to perturbations in the position of the cluster centre. The EHOP method also obviates the need for parameterizing the interactions between the system atoms and the passivating atoms. The method is useful for cluster calculations of non-periodic defects in large systems and for hybrid schemes that simulate large systems by treating finite regions with a quantum-mechanical model, coupled to an interatomic potential description of the rest of the system.

Photoinduced nucleation: a novel tool for detecting molecules in air at ultra-low concentrations

DOEpatents

Katz, Joseph L.; Lihavainen, Heikki; Rudek, Markus M.; Salter, Brian C.

2002-01-01

A method and apparatus for determining the presence of molecules in a gas at concentrations of less than about 100 ppb. Light having wavelengths in the range from about 200 nm to about 350 nm is used to illuminate a flowing sample of the gas causing the molecules if present to form clusters. A mixture of the illuminated gas and a vapor is cooled until the vapor is supersaturated so that there is a small rate of homogeneous nucleation. The supersaturated vapor condenses on the clusters thus causing the clusters to grow to a size sufficient to be counted by light scattering and then the clusters are counted.

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

Nguyen, Duc; Girolami, Gregory S.; Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801

Direct visualization of the dynamics of structural glasses and amorphous solids on the sub-nanometer scale provides rich information unavailable from bulk or conventional single molecule techniques. We study the surface of hafnium diboride, a conductive ultrahigh temperature ceramic material that can be grown in amorphous films. Our scanning tunneling movies have a second-to-hour dynamic range and single-point current measurements extend that to the millisecond-to-minute time scale. On the a-HfB{sub 2} glass surface, two-state hopping of 1–2 nm diameter cooperatively rearranging regions or “clusters” occurs from sub-milliseconds to hours. We characterize individual clusters in detail through high-resolution (<0.5 nm) imaging, scanning tunnelingmore » spectroscopy and voltage modulation, ruling out individual atoms, diffusing adsorbates, or pinned charges as the origin of the observed two-state hopping. Smaller clusters are more likely to hop, larger ones are more likely to be immobile. HfB{sub 2} has a very high bulk glass transition temperature T{sub g}, and we observe no three-state hopping or sequential two-state hopping previously seen on lower T{sub g} glass surfaces. The electronic density of states of clusters does not change when they hop up or down, allowing us to calibrate an accurate relative z-axis scale. By directly measuring and histogramming single cluster vertical displacements, we can reconstruct the local free energy landscape of individual clusters, complete with activation barrier height, a reaction coordinate in nanometers, and the shape of the free energy landscape basins between which hopping occurs. The experimental images are consistent with the compact shape of α-relaxors predicted by random first order transition theory, whereas the rapid hopping rate, even taking less confined motion at the surface into account, is consistent with β-relaxations. We make a proposal of how “mixed” features can show up in surface dynamics of glasses.« less

Model of large volumetric capacitance in graphene supercapacitors based on ion clustering

NASA Astrophysics Data System (ADS)

Skinner, Brian; Fogler, M. M.; Shklovskii, B. I.

2011-12-01

Electric double-layer supercapacitors (SCs) are promising devices for high-power energy storage based on the reversible absorption of ions into porous conducting electrodes. Graphene is a particularly good candidate for the electrode material in SCs due to its high conductivity and large surface area. In this paper, we consider SC electrodes made from a stack of graphene sheets with randomly inserted spacer molecules. We show that the large volumetric capacitances C≳100F/cm3 observed experimentally can be understood as a result of collective intercalation of ions into the graphene stack and the accompanying nonlinear screening by graphene electrons that renormalizes the charge of the ion clusters.

A model of large volumetric capacitance in graphene supercapacitors based on ion clustering

NASA Astrophysics Data System (ADS)

Skinner, Brian; Fogler, Michael; Shklovskii, Boris

2012-02-01

Electric double layer supercapacitors are promising devices for high-power energy storage based on the reversible absorption of ions into porous, conducting electrodes. Graphene is a particularly good candidate for the electrode material in supercapacitors due to its high conductivity and large surface area. In this paper we consider supercapacitor electrodes made from a stack of graphene sheets with randomly-inserted ``spacer" molecules. We show that the large volumetric capacitances C > 100 F/cm^3 observed experimentally can be understood as a result of collective intercalation of ions into the graphene stack and the accompanying nonlinear screening by graphene electrons that renormalizes the charge of the ion clusters.

A theoretical study of water equilibria: The cluster distribution versus temperature and pressure for (H2O)n, n=1-60, and ice

NASA Astrophysics Data System (ADS)

Lenz, Annika; Ojamäe, Lars

2009-10-01

The size distribution of water clusters at equilibrium is studied using quantum-chemical calculations in combination with statistical thermodynamics. The necessary energetic data is obtained by quantum-chemical B3LYP computations and through extrapolations from the B3LYP results for the larger clusters. Clusters with up to 60 molecules are included in the equilibrium computations. Populations of different cluster sizes are calculated using both an ideal gas model with noninteracting clusters and a model where a correction for the interaction energy is included analogous to the van der Waals law. In standard vapor the majority of the water molecules are monomers. For the ideal gas model at 1 atm large clusters [56-mer (0-120 K) and 28-mer (100-260 K)] dominate at low temperatures and separate to smaller clusters [21-22-mer (170-280 K) and 4-6-mer (270-320 K) and to monomers (300-350 K)] when the temperature is increased. At lower pressure the transition from clusters to monomers lies at lower temperatures and fewer cluster sizes are formed. The computed size distribution exhibits enhanced peaks for the clusters consisting of 21 and 28 water molecules; these sizes are for protonated water clusters often referred to as magic numbers. If cluster-cluster interactions are included in the model the transition from clusters to monomers is sharper (i.e., occurs over a smaller temperature interval) than when the ideal-gas model is used. Clusters with 20-22 molecules dominate in the liquid region. When a large icelike cluster is included it will dominate for temperatures up to 325 K for the noninteracting clusters model. Thermodynamic properties (Cp, ΔH) were calculated with in general good agreement with experimental values for the solid and gas phase. A formula for the number of H-bond topologies in a given cluster structure is derived. For the 20-mer it is shown that the number of topologies contributes to making the population of dodecahedron-shaped cluster larger than that of a lower-energy fused prism cluster at high temperatures.

A theoretical study of water equilibria: the cluster distribution versus temperature and pressure for (H2O)n, n = 1-60, and ice.

PubMed

Lenz, Annika; Ojamäe, Lars

2009-10-07

The size distribution of water clusters at equilibrium is studied using quantum-chemical calculations in combination with statistical thermodynamics. The necessary energetic data is obtained by quantum-chemical B3LYP computations and through extrapolations from the B3LYP results for the larger clusters. Clusters with up to 60 molecules are included in the equilibrium computations. Populations of different cluster sizes are calculated using both an ideal gas model with noninteracting clusters and a model where a correction for the interaction energy is included analogous to the van der Waals law. In standard vapor the majority of the water molecules are monomers. For the ideal gas model at 1 atm large clusters [56-mer (0-120 K) and 28-mer (100-260 K)] dominate at low temperatures and separate to smaller clusters [21-22-mer (170-280 K) and 4-6-mer (270-320 K) and to monomers (300-350 K)] when the temperature is increased. At lower pressure the transition from clusters to monomers lies at lower temperatures and fewer cluster sizes are formed. The computed size distribution exhibits enhanced peaks for the clusters consisting of 21 and 28 water molecules; these sizes are for protonated water clusters often referred to as magic numbers. If cluster-cluster interactions are included in the model the transition from clusters to monomers is sharper (i.e., occurs over a smaller temperature interval) than when the ideal-gas model is used. Clusters with 20-22 molecules dominate in the liquid region. When a large icelike cluster is included it will dominate for temperatures up to 325 K for the noninteracting clusters model. Thermodynamic properties (C(p), DeltaH) were calculated with in general good agreement with experimental values for the solid and gas phase. A formula for the number of H-bond topologies in a given cluster structure is derived. For the 20-mer it is shown that the number of topologies contributes to making the population of dodecahedron-shaped cluster larger than that of a lower-energy fused prism cluster at high temperatures.

Asymmetric Top Rotors in Superfluid Para-Hydrogen Nano-Clusters

NASA Astrophysics Data System (ADS)

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.

Theoretical study of adsorption of nitrogen-containing environmental contaminants on kaolinite surfaces.

PubMed

Scott, Andrea Michalkova; Burns, Elizabeth A; Hill, Frances C

2014-08-01

The adsorption of nitrogen-containing compounds (NCCs) including 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT), 2,4-dinitroanisole (DNAN), and 3-nitro-1,2,4-triazol-5-one (NTO) on kaolinite surfaces was investigated. The M06-2X and M06-2X-D3 density functionals were applied with the cluster approximation. Several different positions of NCCs relative to the adsorption sites of kaolinite were examined, including NCCs in perpendicular and parallel orientation toward both surface models of kaolinite. The binding between the target molecules and kaolinite surfaces was analyzed and bond energies were calculated applying the atoms in molecules (AIM) method. All NCCs were found to prefer a parallel orientation toward both kaolinite surfaces, and were bound more strongly to the octahedral than to the tetrahedral site. TNT exhibited the strongest interaction with the octahedral surface and DNAN with the tetrahedral surface of kaolinite. Hydrogen bonding was shown to be the dominant non-covalent interaction for NCCs interacting with the octahedral surface of kaolinite with a small stabilizing effect of dispersion interactions. In the case of adsorption on the tetrahedral surface, kaolonite-NCC binding was shown to be governed by the balance between hydrogen bonds and dispersion forces. The presence of water as a solvent leads to a significant decrease in the adsorption strength for all studied NCCs interacting with both kaolinite surfaces.

Enhanced Electromagnetic and Chemical/Biological Sensing. Properties of Atomic Cluster-Derived Materials

DTIC Science & Technology

2003-02-24

electron injection at interfaces, analysis of the voltage dependence of the electrostatic potential across molecules, the nature of binding at the...nanoscale titania into a metallic surface), analysis of the so-called band lineup between the molecular levels and the Fermi levels of the metal...observe the CNT’s in the electron microscope with the possibility to manipulate them externally and to apply potentials to them. These new

Scrutinizing human MHC polymorphism: Supertype analysis using Poisson-Boltzmann electrostatics and clustering.

PubMed

Mumtaz, Shahzad; Nabney, Ian T; Flower, Darren R

2017-10-01

Peptide-binding MHC proteins are thought the most variable across the human population; the extreme MHC polymorphism observed is functionally important and results from constrained divergent evolution. MHCs have vital functions in immunology and homeostasis: cell surface MHC class I molecules report cell status to CD8+ T cells, NKT cells and NK cells, thus playing key roles in pathogen defence, as well as mediating smell recognition, mate choice, Adverse Drug Reactions, and transplantation rejection. MHC peptide specificity falls into several supertypes exhibiting commonality of binding. It seems likely that other supertypes exist relevant to other functions. Since comprehensive experimental characterization is intractable, structure-based bioinformatics is the only viable solution. We modelled functional MHC proteins by homology and used calculated Poisson-Boltzmann electrostatics projected from the top surface of the MHC as multi-dimensional descriptors, analysing them using state-of-the-art dimensionality reduction techniques and clustering algorithms. We were able to recover the 3 MHC loci as separate clusters and identify clear sub-groups within them, vindicating unequivocally our choice of both data representation and clustering strategy. We expect this approach to make a profound contribution to the study of MHC polymorphism and its functional consequences, and, by extension, other burgeoning structural systems, such as GPCRs. Copyright © 2017 Elsevier Inc. All rights reserved.

High Level ab initio Predictions of the Energetics of mCO2•(H2O)n (n = 1-3, m = 1-12) Clusters

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

Thanthiriwatte, Sahan; Duke, Jessica R.; Jackson, Virgil E.

Electronic structure calculations at the correlated molecular orbital theory and density functional theory levels have been used to generate a reliable set of clustering energies for up to three water molecules in carbon dioxide clusters up to n = 12. The structures and energetics are dominated by Lewis acid-base interactions with hydrogen bonding interactions playing a lesser energetic role. The actual binding energies are somewhat larger than might be expected. The correlated molecular orbital MP2 method and density functional theory with the ωB97X exchange-correlation functional provide good results for the energetics of the clusters but the B3LYP and ωB97X-D functionalsmore » do not. Seven CO2 molecules form the first solvent shell about a single H2O with four CO2 molecules interacting with the H2O via Lewis acid-base interactions, two CO2 interacting with the H2O by hydrogen bonds, and the seventh CO2 completing the shell. The Lewis acid-base and weak hydrogen bond interactions between the water molecules and the CO2 molecules are strong enough to disrupt the trimer ring configuration for as few as seven CO2 molecules. Calculated 13C NMR chemical shifts for mCO2•(H2O)n show little change with respect to the number of H2O or CO2 molecules in the cluster. The O-H stretching frequencies do exhibit shifts that can provide information about the interactions between water and CO2 molecules.« less

Classification of ligand molecules in PDB with graph match-based structural superposition.

PubMed

Shionyu-Mitsuyama, Clara; Hijikata, Atsushi; Tsuji, Toshiyuki; Shirai, Tsuyoshi

2016-12-01

The fast heuristic graph match algorithm for small molecules, COMPLIG, was improved by adding a structural superposition process to verify the atom-atom matching. The modified method was used to classify the small molecule ligands in the Protein Data Bank (PDB) by their three-dimensional structures, and 16,660 types of ligands in the PDB were classified into 7561 clusters. In contrast, a classification by a previous method (without structure superposition) generated 3371 clusters from the same ligand set. The characteristic feature in the current classification system is the increased number of singleton clusters, which contained only one ligand molecule in a cluster. Inspections of the singletons in the current classification system but not in the previous one implied that the major factors for the isolation were differences in chirality, cyclic conformations, separation of substructures, and bond length. Comparisons between current and previous classification systems revealed that the superposition-based classification was effective in clustering functionally related ligands, such as drugs targeted to specific biological processes, owing to the strictness of the atom-atom matching.

Conformational and functional similarities between glutaredoxin and thioredoxins.

PubMed Central

Eklund, H; Cambillau, C; Sjöberg, B M; Holmgren, A; Jörnvall, H; Höög, J O; Brändén, C I

1984-01-01

The tertiary structures of thioredoxin from Escherichia coli and bacteriophage T4 have been compared and aligned giving a common fold of 68 C alpha atoms with a root mean square difference of 2.6 A. The amino acid sequence of glutaredoxin has been aligned to those of the thioredoxins assuming that glutaredoxin has the same common fold. A model of the glutaredoxin molecule was built on a vector display using this alignment and the T4 thioredoxin tertiary structure. By comparison of the model with those of the thioredoxins, we have identified a molecular surface area on one side of the redox-active S-S bridge which we suggest is the binding area of these molecules for redox interactions with other proteins. This area comprises residues 33-34, 75-76 and 91-93 in E. coli thioredoxin; 15-16, 65-66 and 76-78 in T4 thioredoxin and 12-13, 59-60 and 69-71 in glutaredoxin. In all three molecules, this part of the surface is flat and hydrophobic. Charged groups are completely absent. In contrast, there is a cluster of charged groups on the other side of the S-S bridge which we suggest participates in the mechanisms of the redox reactions. In particular, a lysine residue close to an aromatic ring is conserved in all molecules. PMID:6378624

Biomimetic Nanoarchitectures for the Study of T Cell Activation with Single-Molecule Control

NASA Astrophysics Data System (ADS)

Cai, Haogang

Physical factors in the environment of a cell affect its function and behavior in a variety of ways. There is increasing evidence that, among these factors, the geometric arrangement of receptor ligands plays an important role in setting the conditions for critical cellular processes. The goal of this thesis is to develop new techniques for probing the role of extracellular ligand geometry, with a focus on T cell activation. In this work, top-down molecular-scale nanofabrication and bottom-up selective self-assembly were combined in order to present functional nanomaterials (primarily biomolecules) on a surface with precise spatial control and single-molecule resolution. Such biomolecule nanoarrays are becoming an increasingly important tool in surface-based in vitro assays for biosensing, molecular and cellular studies. The nanoarrays consist of metallic nanodots patterned on glass coverslips using electron beam and nanoimprint lithography, combined with self-aligned pattern transfer. The nanodots were then used as anchors for the immobilization of biological ligands, and backfilled with a protein-repellent passivation layer of polyethylene glycol. The passivation efficiency was improved to minimize nonspecific adsorption. In order to ensure true single-molecule control, we developed an on-chip protocol to measure the molecular occupancy of nanodot arrays based on fluorescence photobleaching, while accounting for quenching effects by plasmonic absorption. We found that the molecular occupancy can be interpreted as a packing problem, with the solution depending on the nanodot size and the concentration of self-assembly reagents, where the latter can be easily adjusted to control the molecular occupancy according to the dot size. The optimized nanoarrays were used as biomimetic architectures for the study of T cell activation with single-molecule control. T cell activation involves an elaborate arrangement of signaling, adhesion, and costimulatory molecules 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.

Electron wavepacket dynamics in highly quasi-degenerate coupled electronic states: a theory for chemistry where the notion of adiabatic potential energy surface loses the sense.

PubMed

Yonehara, Takehiro; Takatsuka, Kazuo

2012-12-14

We develop a theory and the method of its application for chemical dynamics in systems, in which the adiabatic potential energy hyper-surfaces (PES) are densely quasi-degenerate to each other in a wide range of molecular geometry. Such adiabatic electronic states tend to couple each other through strong nonadiabatic interactions. Technically, therefore, it is often extremely hard to accurately single out the individual PES in those systems. Moreover, due to the mutual nonadiabatic couplings that may spread wide in space and due to the energy-time uncertainty relation, the notion of the isolated and well-defined potential energy surface should lose the sense. On the other hand, such dense electronic states should offer a very interesting molecular field in which chemical reactions to proceed in characteristic manners. However, to treat these systems, the standard theoretical framework of chemical reaction dynamics, which starts from the Born-Oppenheimer approximation and ends up with quantum nuclear wavepacket dynamics, is not very useful. We here explore this problem with our developed nonadiabatic electron wavepacket theory, which we call the phase-space averaging and natural branching (PSANB) method [T. Yonehara and K. Takatsuka, J. Chem. Phys. 129, 134109 (2008)], or branching-path representation, in which the packets are propagated in time along the non-Born-Oppenheimer branching paths. In this paper, after outlining the basic theory, we examine using a one-dimensional model how well the PSANB method works with such densely quasi-degenerate nonadiabatic systems. To do so, we compare the performance of PSANB with the full quantum mechanical results and those given by the fewest switches surface hopping (FSSH) method, which is known to be one of the most reliable and flexible methods to date. It turns out that the PSANB electron wavepacket approach actually yields very good results with far fewer initial sampling paths. Then we apply the electron wavepacket dynamics in path-branching representation and the so-called semiclassical Ehrenfest theory to a hydrogen molecule embedded in twelve membered boron cluster (B(12)) in excited states, which are densely quasi-degenerate due to the vacancy in 2p orbitals of boron atom [1s(2)2s(2)2p(1)]. Bond dissociation of the hydrogen molecule quickly takes place in the cluster and the resultant hydrogen atoms are squeezed out to the surface of the cluster. We further study collision dynamics between H(2) and B(12), which also gives interesting phenomena. The present study suggests an interesting functionality of the boron clusters.

Sequential evaporation of water molecules from protonated water clusters: measurement of the velocity distributions of the evaporated molecules and statistical analysis.

PubMed

Berthias, F; Feketeová, L; Abdoul-Carime, H; Calvo, F; Farizon, B; Farizon, M; Märk, T D

2018-06-22

Velocity distributions of neutral water molecules evaporated after collision induced dissociation of protonated water clusters H+(H2O)n≤10 were measured using the combined correlated ion and neutral fragment time-of-flight (COINTOF) and velocity map imaging (VMI) techniques. As observed previously, all measured velocity distributions exhibit two contributions, with a low velocity part identified by statistical molecular dynamics (SMD) simulations as events obeying the Maxwell-Boltzmann statistics and a high velocity contribution corresponding to non-ergodic events in which energy redistribution is incomplete. In contrast to earlier studies, where the evaporation of a single molecule was probed, the present study is concerned with events involving the evaporation of up to five water molecules. In particular, we discuss here in detail the cases of two and three evaporated molecules. Evaporation of several water molecules after CID can be interpreted in general as a sequential evaporation process. In addition to the SMD calculations, a Monte Carlo (MC) based simulation was developed allowing the reconstruction of the velocity distribution produced by the evaporation of m molecules from H+(H2O)n≤10 cluster ions using the measured velocity distributions for singly evaporated molecules as the input. The observed broadening of the low-velocity part of the distributions for the evaporation of two and three molecules as compared to the width for the evaporation of a single molecule results from the cumulative recoil velocity of the successive ion residues as well as the intrinsically broader distributions for decreasingly smaller parent clusters. Further MC simulations were carried out assuming that a certain proportion of non-ergodic events is responsible for the first evaporation in such a sequential evaporation series, thereby allowing to model the entire velocity distribution.

Gas cluster ion beam for the characterization of organic materials in submarine basalts as Mars analogs

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

Sano, Naoko, E-mail: naoko.sano@ncl.ac.uk; Barlow, Anders J.; Cumpson, Peter J.

The solar system contains large quantities of organic compounds that can form complex molecular structures. The processing of organic compounds by biological systems leads to molecules with distinctive structural characteristics; thus, the detection and characterization of organic materials could lead to a high degree of confidence in the existence of extra-terrestrial life. Given the nature of the surface of most planetary bodies in the solar system, evidence of life is more likely to be found in the subsurface where conditions are more hospitable. Basalt is a common rock throughout the solar system and the primary rock type on Mars andmore » Earth. Basalt is therefore a rock type that subsurface life might exploit and as such a suitable material for the study of methods required to detect and analyze organic material in rock. Telluric basalts from Earth represent an analog for extra-terrestrial rocks where the indigenous organic matter could be analyzed for molecular biosignatures. This study focuses on organic matter in the basalt with the use of surface analysis techniques utilizing Ar gas cluster ion beams (GCIB); time of flight secondary ion mass spectrometry (ToF-SIMS), and x-ray photoelectron spectroscopy (XPS), to characterize organic molecules. Tetramethylammonium hydroxide (TMAH) thermochemolysis was also used to support the data obtained using the surface analysis techniques. The authors demonstrate that organic molecules were found to be heterogeneously distributed within rock textures. A positive correlation was observed to exist between the presence of microtubule textures in the basalt and the organic compounds detected. From the results herein, the authors propose that ToF-SIMS with an Ar GCIB is effective at detecting organic materials in such geological samples, and ToF-SIMS combined with XPS and TMAH thermochemolysis may be a useful approach in the study of extra-terrestrial organic material and life.« less

[Application of Kohonen Self-Organizing Feature Maps in QSAR of human ADMET and kinase data sets].

PubMed

Hegymegi-Barakonyi, Bálint; Orfi, László; Kéri, György; Kövesdi, István

2013-01-01

QSAR predictions have been proven very useful in a large number of studies for drug design, such as kinase inhibitor design as targets for cancer therapy, however the overall predictability often remains unsatisfactory. To improve predictability of ADMET features and kinase inhibitory data, we present a new method using Kohonen's Self-Organizing Feature Map (SOFM) to cluster molecules based on explanatory variables (X) and separate dissimilar ones. We calculated SOFM clusters for a large number of molecules with human ADMET and kinase inhibitory data, and we showed that chemically similar molecules were in the same SOFM cluster, and within such clusters the QSAR models had significantly better predictability. We used also target variables (Y, e.g. ADMET) jointly with X variables to create a novel type of clustering. With our method, cells of loosely coupled XY data could be identified and separated into different model building sets.

Theoretical investigation of interaction of sorbitol molecules with alcohol dehydrogenase in aqueous solution using molecular dynamics simulation.

PubMed

Bahrami, Homayoon; Zahedi, Mansour; Moosavi-Movahedi, Ali Akbar; Azizian, Homa; Amanlou, Massoud

2011-03-01

The nature of protein-sorbitol-water interaction in solution at the molecular level, has been investigated using molecular dynamics simulations. In order to do this task, two molecular dynamics simulations of the protein ADH in solution at room temperature have been carried out, one in the presence (about 0.9 M) and another in the absence of sorbitol. The results show that the sorbitol molecules cluster and move toward the protein, and form hydrogen bonds with protein. Also, coating by sorbitol reduces the conformational fluctuations of the protein compared to the sorbitol-free system. Thus, it is concluded that at moderate concentration of sorbitol solution, sorbitol molecules interact with ADH via many H-bonds that prevent the protein folding. In fact, at more concentrated sorbitol solution, water and sorbitol molecules accumulate around the protein surface and form a continuous space-filling network to reduce the protein flexibility. Namely, in such solution, sorbitol molecules can stabilize a misfolded state of ADH, and prevent the protein from folding to its native structure.

Partially linearized external models to active-space coupled-cluster through connected hextuple excitations.

PubMed

Xu, Enhua; Ten-No, Seiichiro L

2018-06-05

Partially linearized external models to active-space coupled-cluster through hextuple excitations, for example, CC{SDtqph} L , CCSD{tqph} L , and CCSD{tqph} hyb, are implemented and compared with the full active-space CCSDtqph. The computational scaling of CCSDtqph coincides with that for the standard coupled-cluster singles and doubles (CCSD), yet with a much large prefactor. The approximate schemes to linearize the external excitations higher than doubles are significantly cheaper than the full CCSDtqph model. These models are applied to investigate the bond dissociation energies of diatomic molecules (HF, F 2 , CuH, and CuF), and the potential energy surfaces of the bond dissociation processes of HF, CuH, H 2 O, and C 2 H 4 . Among the approximate models, CCSD{tqph} hyb provides very accurate descriptions compared with CCSDtqph for all of the tested systems. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Computational evaluation of sub-nanometer cluster activity of singly exposed copper atom with various coordinative environment in catalytic CO2 transformation

NASA Astrophysics Data System (ADS)

Shanmugam, Ramasamy; Thamaraichelvan, Arunachalam; Ganesan, Tharumeya Kuppusamy; Viswanathan, Balasubramanian

2017-02-01

Metal cluster, at sub-nanometer level has a unique property in the activation of small molecules, in contrast to that of bulk surface. In the present work, singly exposed active site of copper metal cluster at sub-nanometer level was designed to arrive at the energy minimised configurations, binding energy, electrostatic potential map, frontier molecular orbitals and partial density of states. The ab initio molecular dynamics was carried out to probe the catalytic nature of the cluster. Further, the stability of the metal cluster and its catalytic activity in the electrochemical reduction of CO2 to CO were evaluated by means of computational hydrogen electrode via calculation of the free energy profile using DFT/B3LYP level of theory in vacuum. The activity of the cluster is ascertained from the fact that the copper atom, present in a two coordinative environment, performs a more selective conversion of CO2 to CO at an applied potential of -0.35 V which is comparatively lower than that of higher coordinative sites. The present study helps to design any sub-nano level metal catalyst for electrochemical reduction of CO2 to various value added chemicals.

Calculation of the structure of carbon clusters based on fullerene-like C24 and C48 molecules

NASA Astrophysics Data System (ADS)

Krylova, K. A.; Baimova, Yu. A.; Dmitriev, S. V.; Mulyukov, R. R.

2016-02-01

Equilibrium structures obtained by linking with valence bonds the carbon carcasses of two fullerene-like molecules have been studied by molecular dynamics simulation. In free fullerene, carbon atoms form sp 2 hybridized bonds, but at places of links between fullerenes, sp 3 hybridized bonds are formed, which determines the changes in the properties of such structures. In the literature, the topology of diamond-like phases is described, but equilibrium clusters based on fullerene-like molecules are underexplored. The right angles between the C-C bonds are energetically unfavorable, and the reduction in the energy of clusters in the process of relaxation is connected with the optimization of valence angles, which leads to a reduction in the symmetry of clusters and, in a number of cases, even to disruption of some valence bonds. It is shown that different fashions of linking two fullerenes result in the formation of clusters with different structures and energies. Different initial conditions can lead to different configurations of clusters with the same topology. Among the analyzed clusters, a structure with the minimum potential energy per atom was found. The results of this work contribute to the study of the real structure of carbon clusters.

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

PubMed

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 isolated defects where it involves formation of H3O(+)-acid anion contact ion pairs. This behavior is found in simulations of a model of the ice quasi-liquid layer corresponding to large defect concentrations in crystalline ice. The results are in accord with experiments. (iv) Ionization of acids on wet quartz. A monolayer of water on hydroxylated silica is ordered even at room temperature, but the surface lattice constant differs significantly from that of crystalline ice. The ionization processes of HCl and H2SO4 are of high yield and occur in a few picoseconds. The results are in accord with experimental spectroscopy. (v) Photochemical reactions on water and ice. These simulations require excited state quantum chemical methods. The electronic absorption spectrum of methyl hydroperoxide adsorbed on a large ice cluster is strongly blue-shifted relative to the isolated molecule. The measured and calculated adsorption band low-frequency tails are in agreement. A simple model of photodynamics assumes prompt electronic relaxation of the excited peroxide due to the ice surface. SEMD simulations support this, with the important finding that the photochemistry takes place mainly on the ground state. In conclusion, dynamics simulations using quantum chemical potentials are a useful tool in atmospheric chemistry of water media, capable of comparison with experiment.

An AB Initio Study of SbH_2 and BiH_2: the Renner Effect, Spin-Orbit Coupling, Local Mode Vibrations and Rovibronic Energy Level Clustering in SbH_2

NASA Astrophysics Data System (ADS)

Ostojic, Bojana; Schwerdtfeger, Peter; Bunker, Phil; Jensen, Per

2016-06-01

We present the results of ab initio calculations for the lower electronic states of the Group 15 (pnictogen) dihydrides, SbH_2 and BiH_2. For each of these molecules the two lowest electronic states become degenerate at linearity and are therefore subject to the Renner effect. Spin-orbit coupling is also strong in these two heavy-element containing molecules. For the lowest two electronic states of SbH_2, we construct the three dimensional potential energy surfaces and corresponding dipole moment and transition moment surfaces by multi-reference configuration interaction techniques. Including both the Renner effect and spin-orbit coupling, we calculate term values and simulate the rovibrational and rovibronic spectra of SbH_2. Excellent agreement is obtained with the results of matrix isolation infrared spectroscopic studies and with gas phase electronic spectroscopic studies in absorption [1,2]. For the heavier dihydride BiH_2 we calculate bending potential curves and the spin-orbit coupling constant for comparison. For SbH_2 we further study the local mode vibrational behavior and the formation of rovibronic energy level clusters in high angular momentum states. [1] X. Wang, P. F. Souter and L. Andrews, J. Phys. Chem. A 107, 4244-4249 (2003) [2] N. Basco and K. K. Lee, Spectroscopy Letters 1, 13-15 (1968)

Insulin promotes cell migration by regulating PSA-NCAM

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

Monzo, Hector J.; Coppieters, Natacha; Department of Anatomy and Medical Imaging, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag, 92019, Auckland

Cellular interactions with the extracellular environment are modulated by cell surface polysialic acid (PSA) carried by the neural cell adhesion molecule (NCAM). PSA-NCAM is involved in cellular processes such as differentiation, plasticity, and migration, and is elevated in Alzheimer's disease as well as in metastatic tumour cells. Our previous work demonstrated that insulin enhances the abundance of cell surface PSA by inhibiting PSA-NCAM endocytosis. In the present study we have identified a mechanism for insulin-dependent inhibition of PSA-NCAM turnover affecting cell migration. Insulin enhanced the phosphorylation of the focal adhesion kinase leading to dissociation of αv-integrin/PSA-NCAM clusters, and promoted cellmore » migration. Our results show that αv-integrin plays a key role in the PSA-NCAM turnover process. αv-integrin knockdown stopped PSA-NCAM from being endocytosed, and αv-integrin/PSA-NCAM clusters co-labelled intracellularly with Rab5, altogether indicating a role for αv-integrin as a carrier for PSA-NCAM during internalisation. Furthermore, inhibition of p-FAK caused dissociation of αv-integrin/PSA-NCAM clusters and counteracted the insulin-induced accumulation of PSA at the cell surface and cell migration was impaired. Our data reveal a functional association between the insulin/p-FAK-dependent regulation of PSA-NCAM turnover and cell migration through the extracellular matrix. Most importantly, they identify a novel mechanism for insulin-stimulated cell migration. - Highlights: • Insulin modulates PSA-NCAM turnover through upregulation of p-FAK. • P-FAK modulates αv-integrin/PSA-NCAM clustering. • αv-integrin acts as a carrier for PSA-NCAM endocytosis. • Cell migration is promoted by cell surface PSA. • Insulin promotes PSA-dependent migration in vitro.« less

Molecular dynamics simulations of graphoepitaxy of organic semiconductors, sexithiophene, and pentacene: Molecular-scale mechanisms of organic graphoepitaxy

NASA Astrophysics Data System (ADS)

Ikeda, Susumu

2018-03-01

Molecular dynamics (MD) simulations of the organic semiconductors α-sexithiophene (6T) and pentacene were carried out to clarify the mechanism of organic graphoepitaxy at the molecular level. First, the models of the grooved substrates were made and the surfaces of the inside of the grooves were modified with -OH or -OSi(CH3)3, making the surfaces hydrophilic or hydrophobic. By the MD simulations of 6T, it was found that three stable azimuthal directions exist (0, ˜45, and 90° the angle that the c-axis makes with the groove), being consistent with experimental results. MD simulations of deposition processes of 6T and pentacene were also carried out, and pentacene molecules showed the spontaneous formation of herringbone packing during deposition. Some pentacene molecules stood on the surface and formed a cluster whose a-axis was parallel to the groove. It is expected that a deep understanding of the molecular-scale mechanisms will lead graphoepitaxy to practical applications, improving the performance of organic devices.

Molecular complexes in close and far away

PubMed Central

Klemperer, William; Vaida, Veronica

2006-01-01

In this review, gas-phase chemistry of interstellar media and some planetary atmospheres is extended to include molecular complexes. Although the composition, density, and temperature of the environments discussed are very different, molecular complexes have recently been considered as potential contributors to chemistry. The complexes reviewed include strongly bound aggregates of molecules with ions, intermediate-strength hydrogen bonded complexes (primarily hydrates), and weakly bonded van der Waals molecules. In low-density, low-temperature environments characteristic of giant molecular clouds, molecular synthesis, known to involve gas-phase ion-molecule reactions and chemistry at the surface of dust and ice grains is extended here to involve molecular ionic clusters. At the high density and high temperatures found on planetary atmospheres, molecular complexes contribute to both atmospheric chemistry and climate. Using the observational, laboratory, and theoretical database, the role of molecular complexes in close and far away is discussed. PMID:16740667

Metal cluster chemistry: Structure and stereochemistry in the polynuclear rhodium hydrides HnRhn[P(OR)3]2n

PubMed Central

Brown, R. K.; Williams, J. M.; Fredrich, M. F.; Day, V. W.; Sivak, A. J.; Muetterties, E. L.

1979-01-01

Crystallographic analyses of x-ray and neutron diffraction data have provided a definitive structural representation of {HRh[P(O-i-C3H7)3]2}2 and {HRh[P(OCH3)3]2}3. These polynuclear hydrides are generated from square planar H2Rh[P(OR)3]2 units by edge (hydrogen atom) sharing and by vertex (hydrogen atom) sharing to form the dimeric and trimeric structures, respectively. The square-planar units are held together through four-center and three-center two-electron Rh—H—Rh bonds in the dimer and trimer, respectively. The dimer and trimer molecules each add one molecule of hydrogen to form H[(i-C3H7O)3P]2RhH3Rh [P(O-i-C3H7)3]2 and H5Rh3[P(OCH3)3]6, respectively. NMR spectral information has served to define the stereochemical features of these polyhydrides. The significance of this chemistry in the metal cluster-metal surface analogy is described. PMID:16592645

Understanding the high pressure properties of molecular solids and molecular surfaces deposited on hetrogeneous substrates

NASA Technical Reports Server (NTRS)

Etters, R. D.

1985-01-01

Work directed toward understanding the high pressure properties of molecular solids and molecular surfaces deposited on hetrogeneous substrates is reported. The motivation, apart from expanding our basic knowledge about these systems, was to understand and predict the properties of new materials synthesized at high pressure, including pressure induced metallic and superconducting states. As a consequence, information about the states of matter of the Jovian planets and their satellites, which are natural high pressure laboratories was also provided. The work on molecular surfaces and finite two and three dimensional clusters of atoms and molecules was connected with the composition and behavior of planetary atmospheres and on the processes involved in forming surface layers, which is vital to the development of composite materials and microcircuitry.

Enhanced diffusion on oscillating surfaces through synchronization

NASA Astrophysics Data System (ADS)

Wang, Jin; Cao, Wei; Ma, Ming; Zheng, Quanshui

2018-02-01

The diffusion of molecules and clusters under nanoscale confinement or absorbed on surfaces is the key controlling factor in dynamical processes such as transport, chemical reaction, or filtration. Enhancing diffusion could benefit these processes by increasing their transport efficiency. Using a nonlinear Langevin equation with an extensive number of simulations, we find a large enhancement in diffusion through surface oscillation. For helium confined in a narrow carbon nanotube, the diffusion enhancement is estimated to be over three orders of magnitude. A synchronization mechanism between the kinetics of the particles and the oscillating surface is revealed. Interestingly, a highly nonlinear negative correlation between diffusion coefficient and temperature is predicted based on this mechanism, and further validated by simulations. Our results provide a general and efficient method for enhancing diffusion, especially at low temperatures.

An experimental point of view on hydration/solvation in halophilic proteins

PubMed Central

Talon, Romain; Coquelle, Nicolas; Madern, Dominique; Girard, Eric

2014-01-01

Protein-solvent interactions govern the behaviors of proteins isolated from extreme halophiles. In this work, we compared the solvent envelopes of two orthologous tetrameric malate dehydrogenases (MalDHs) from halophilic and non-halophilic bacteria. The crystal structure of the MalDH from the non-halophilic bacterium Chloroflexus aurantiacus (Ca MalDH) solved, de novo, at 1.7 Å resolution exhibits numerous water molecules in its solvation shell. We observed that a large number of these water molecules are arranged in pentagonal polygons in the first hydration shell of Ca MalDH. Some of them are clustered in large networks, which cover non-polar amino acid surface. The crystal structure of MalDH from the extreme halophilic bacterium Salinibacter ruber (Sr) solved at 1.55 Å resolution shows that its surface is strongly enriched in acidic amino acids. The structural comparison of these two models is the first direct observation of the relative impact of acidic surface enrichment on the water structure organization between a halophilic protein and its non-adapted counterpart. The data show that surface acidic amino acids disrupt pentagonal water networks in the hydration shell. These crystallographic observations are discussed with respect to halophilic protein behaviors in solution PMID:24600446

An experimental point of view on hydration/solvation in halophilic proteins.

PubMed

Talon, Romain; Coquelle, Nicolas; Madern, Dominique; Girard, Eric

2014-01-01

Protein-solvent interactions govern the behaviors of proteins isolated from extreme halophiles. In this work, we compared the solvent envelopes of two orthologous tetrameric malate dehydrogenases (MalDHs) from halophilic and non-halophilic bacteria. The crystal structure of the MalDH from the non-halophilic bacterium Chloroflexus aurantiacus (Ca MalDH) solved, de novo, at 1.7 Å resolution exhibits numerous water molecules in its solvation shell. We observed that a large number of these water molecules are arranged in pentagonal polygons in the first hydration shell of Ca MalDH. Some of them are clustered in large networks, which cover non-polar amino acid surface. The crystal structure of MalDH from the extreme halophilic bacterium Salinibacter ruber (Sr) solved at 1.55 Å resolution shows that its surface is strongly enriched in acidic amino acids. The structural comparison of these two models is the first direct observation of the relative impact of acidic surface enrichment on the water structure organization between a halophilic protein and its non-adapted counterpart. The data show that surface acidic amino acids disrupt pentagonal water networks in the hydration shell. These crystallographic observations are discussed with respect to halophilic protein behaviors in solution.

Theoretical studies of large water clusters: (H2O)28, (H2O)29, (H2O)30, and (H2O)31 hexakaidecahedral structures

NASA Astrophysics Data System (ADS)

Khan, Arshad

1997-04-01

The 28, 29, 30, and 31 mer hexakaidecahedral water clusters were studied by applying the intermediate neglect of differential overlap self-consistent field restricted Hartree-Fock method (INDO SCF RHF) after parametrization for H and O atoms. The most stable 29 and 30 mer clusters have one and two water molecules, respectively within the cavity of the distorted hexakaidecahedral cage with stabilization energy/monomer values of around 10.9 and 11.0 kcal, respectively. The 31 mer cluster with three water molecules within the cavity is less stable than the isomer with two molecules within the cavity and the third one bonded outside of the cage by around 3 kcal/mol.

Unconventional Current Scaling and Edge Effects for Charge Transport through Molecular Clusters

PubMed Central

2017-01-01

Metal–molecule–metal junctions are the key components of molecular electronics circuits. Gaining a microscopic understanding of their conducting properties is central to advancing the field. In the present contribution, we highlight the fundamental differences between single-molecule and ensemble junctions focusing on the fundamentals of transport through molecular clusters. In this way, we elucidate the collective behavior of parallel molecular wires, bridging the gap between single molecule and large-area monolayer electronics, where even in the latter case transport is usually dominated by finite-size islands. On the basis of first-principles charge-transport simulations, we explain why the scaling of the conductivity of a junction has to be distinctly nonlinear in the number of molecules it contains. Moreover, transport through molecular clusters is found to be highly inhomogeneous with pronounced edge effects determined by molecules in locally different electrostatic environments. These effects are most pronounced for comparably small clusters, but electrostatic considerations show that they prevail also for more extended systems. PMID:29043825

Co-existence of monomers and clusters in concentrated protein solutions

NASA Astrophysics Data System (ADS)

Chinchalikar, Akshay J.; Kumar, Sugam; Aswal, V. K.; Callow, P.; Wagh, A. G.

2012-06-01

Small-angle neutron scattering (SANS) measurements have been performed on concentrated protein solutions in order to study aggregation of lysozyme molecules at different pH. The variation of correlation peak in concentration (C) dependent SANS data shows deviation from C1/3 behavior suggesting the aggregation phenomena in these systems. The aggregates or clusters coexist along with monomers with cluster fraction proportional to protein concentration. The clustering is also favored at higher pH approaching isoelectric point (pI) because of decrease in charge on the protein molecule.

CO2 Cluster Ion Beam, an Alternative Projectile for Secondary Ion Mass Spectrometry

NASA Astrophysics Data System (ADS)

Tian, Hua; Maciążek, Dawid; Postawa, Zbigniew; Garrison, Barbara J.; Winograd, Nicholas

2016-09-01

The emergence of argon-based gas cluster ion beams for SIMS experiments opens new possibilities for molecular depth profiling and 3D chemical imaging. These beams generally leave less surface chemical damage and yield mass spectra with reduced fragmentation compared with smaller cluster projectiles. For nanoscale bioimaging applications, however, limited sensitivity due to low ionization probability and technical challenges of beam focusing remain problematic. The use of gas cluster ion beams based upon systems other than argon offer an opportunity to resolve these difficulties. Here we report on the prospects of employing CO2 as a simple alternative to argon. Ionization efficiency, chemical damage, sputter rate, and beam focus are investigated on model compounds using a series of CO2 and Ar cluster projectiles (cluster size 1000-5000) with the same mass. The results show that the two projectiles are very similar in each of these aspects. Computer simulations comparing the impact of Ar2000 and (CO2)2000 on an organic target also confirm that the CO2 molecules in the cluster projectile remain intact, acting as a single particle of m/z 44. The imaging resolution employing CO2 cluster projectiles is improved by more than a factor of two. The advantage of CO2 versus Ar is also related to the increased stability which, in addition, facilitates the operation of the gas cluster ion beams (GCIB) system at lower backing pressure.

Hybrid quantum and molecular mechanics embedded cluster models for chemistry on silicon and silicon carbide surfaces

NASA Astrophysics Data System (ADS)

Shoemaker, James Richard

Fabrication of silicon carbide (SiC) semiconductor devices are of interest for aerospace applications because of their high-temperature tolerance. Growth of an insulating SiO2 layer on SiC by oxidation is a poorly understood process, and sometimes produces interface defects that degrade device performance. Accurate theoretical models of surface chemistry, using quantum mechanics (QM), do not exist because of the huge computational cost of solving Schrodinger's equation for a molecular cluster large enough to represent a surface. Molecular mechanics (MM), which describes a molecule as a collection of atoms interacting through classical potentials, is a fast computational method, good at predicting molecular structure, but cannot accurately model chemical reactions. A new hybrid QM/MM computational method for surface chemistry was developed and applied to silicon and SiC surfaces. The addition of MM steric constraints was shown to have a large effect on the energetics of O atom adsorption on SiC. Adsorption of O atoms on Si-terminated SiC(111) favors above surface sites, in contrast to Si(111), but favors subsurface adsorption sites on C- terminated SiC(111). This difference, and the energetics of C atom etching via CO2 desorption, can explain the observed poor performance of SiC devices in which insulating layers were grown on C-terminated surfaces.

A spherical electron cloud hopping model for studying product branching ratios of dissociative recombination.

PubMed

Yu, Hua-Gen

2008-05-21

A spherical electron cloud hopping (SECH) model is proposed to study the product branching ratios of dissociative recombination (DR) of polyatomic systems. In this model, the fast electron-captured process is treated as an instantaneous hopping of a cloud of uniform spherical fractional point charges onto a target M+q ion (or molecule). The sum of point charges (-1) simulates the incident electron. The sphere radius is determined by a critical distance (Rc eM) between the incoming electron (e-) and the target, at which the potential energy of the e(-)-M+q system is equal to that of the electron-captured molecule M+q(-1) in a symmetry-allowed electronic state with the same structure as M(+q). During the hopping procedure, the excess energies of electron association reaction are dispersed in the kinetic energies of M+q(-1) atoms to conserve total energy. The kinetic energies are adjusted by linearly adding atomic momenta in the direction of driving forces induced by the scattering electron. The nuclear dynamics of the resultant M+q(-1) molecule are studied by using a direct ab initio dynamics method on the adiabatic potential energy surface of M+q(-1), or together with extra adiabatic surface(s) of M+q(-1). For the latter case, the "fewest switches" surface hopping algorithm of Tully was adapted to deal with the nonadiabaticity in trajectory propagations. The SECH model has been applied to study the DR of both CH+ and H3O+(H2O)2. The theoretical results are consistent with the experiment. It was found that water molecules play an important role in determining the product branching ratios of the molecular cluster ion.

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

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

Kompanets, V. O.; Lokhman, V. N.; Poydashev, D. G., E-mail: poydashev@isan.troitsk.ru

2016-04-15

The dynamics of photoprocesses induced by femtosecond infrared radiation in free Fe(CO){sub 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){sub 5}{sup +} molecular ion. Subsequent relaxation processes have been analyzed and the results havemore » 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){sub 5}]{sub 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){sub 5}]{sub n} clusters have been estimated.« less

Scanning the potential energy surface for synthesis of dendrimer-wrapped gold clusters: design rules for true single-molecule nanostructures.

PubMed

Thompson, Damien; Hermes, Jens P; Quinn, Aidan J; Mayor, Marcel

2012-04-24

The formation of true single-molecule complexes between organic ligands and nanoparticles is challenging and requires careful design of molecules with size, shape, and chemical properties tailored for the specific nanoparticle. Here we use computer simulations to describe the atomic-scale structure, dynamics, and energetics of ligand-mediated synthesis and interlinking of 1 nm gold clusters. The models help explain recent experimental results and provide insight into how multidentate thioether dendrimers can be employed for synthesis of true single-ligand-nanoparticle complexes and also nanoparticle-molecule-nanoparticle "dumbbell" nanostructures. Electronic structure calculations reveal the individually weak thioether-gold bonds (325 ± 36 meV), which act collectively through the multivalent (multisite) anchoring to stabilize the ligand-nanoparticle complex (∼7 eV total binding energy) and offset the conformational and solvation penalties involved in this "wrapping" process. Molecular dynamics simulations show that the dendrimer is sufficiently flexible to tolerate the strained conformations and desolvation penalties involved in fully wrapping the particle, quantifying the subtle balance between covalent anchoring and noncovalent wrapping in the assembly of ligand-nanoparticle complexes. The computed preference for binding of a single dendrimer to the cluster reveals the prohibitively high dendrimer desolvation barrier (1.5 ± 0.5 eV) to form the alternative double-dendrimer structure. Finally, the models show formation of an additional electron transfer channel between nitrogen and gold for ligands with a central pyridine unit, which gives a stiff binding orientation and explains the recently measured larger interparticle distances for particles synthesized and interlinked using linear ligands with a central pyridine rather than a benzene moiety. The findings stress the importance of organic-inorganic interactions, the control of which is central to the rational engineering and eventual large-scale production of functional building blocks for nano(bio)electronics.

Mapping antigenic motifs in the trypomastigote small surface antigen from Trypanosoma cruzi.

PubMed

Balouz, Virginia; Cámara, María de Los Milagros; Cánepa, Gaspar E; Carmona, Santiago J; Volcovich, Romina; Gonzalez, Nicolás; Altcheh, Jaime; Agüero, Fernán; Buscaglia, Carlos A

2015-03-01

The trypomastigote small surface antigen (TSSA) is a mucin-like molecule from Trypanosoma cruzi, the etiological agent of Chagas disease, which displays amino acid polymorphisms in parasite isolates. TSSA expression is restricted to the surface of infective cell-derived trypomastigotes, where it functions as an adhesin and engages surface receptors on the host cell as a prerequisite for parasite internalization. Previous results have established TSSA-CL, the isoform encoded by the CL Brener clone, as an appealing candidate for use in serology-based diagnostics for Chagas disease. Here, we used a combination of peptide- and recombinant protein-based tools to map the antigenic structure of TSSA-CL at maximal resolution. Our results indicate the presence of different partially overlapping B-cell epitopes clustering in the central portion of TSSA-CL, which contains most of the polymorphisms found in parasite isolates. Based on these results, we assessed the serodiagnostic performance of a 21-amino-acid-long peptide that spans TSSA-CL major antigenic determinants, which was similar to the performance of the previously validated glutathione S-transferase (GST)-TSSA-CL fusion molecule. Furthermore, the tools developed for the antigenic characterization of the TSSA antigen were also used to explore other potential diagnostic applications of the anti-TSSA humoral response in Chagasic patients. Overall, our present results provide additional insights into the antigenic structure of TSSA-CL and support this molecule as an excellent target for molecular intervention in Chagas disease. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Mapping Antigenic Motifs in the Trypomastigote Small Surface Antigen from Trypanosoma cruzi

PubMed Central

Balouz, Virginia; Cámara, María de los Milagros; Cánepa, Gaspar E.; Carmona, Santiago J.; Volcovich, Romina; Gonzalez, Nicolás; Altcheh, Jaime; Agüero, Fernán

2015-01-01

The trypomastigote small surface antigen (TSSA) is a mucin-like molecule from Trypanosoma cruzi, the etiological agent of Chagas disease, which displays amino acid polymorphisms in parasite isolates. TSSA expression is restricted to the surface of infective cell-derived trypomastigotes, where it functions as an adhesin and engages surface receptors on the host cell as a prerequisite for parasite internalization. Previous results have established TSSA-CL, the isoform encoded by the CL Brener clone, as an appealing candidate for use in serology-based diagnostics for Chagas disease. Here, we used a combination of peptide- and recombinant protein-based tools to map the antigenic structure of TSSA-CL at maximal resolution. Our results indicate the presence of different partially overlapping B-cell epitopes clustering in the central portion of TSSA-CL, which contains most of the polymorphisms found in parasite isolates. Based on these results, we assessed the serodiagnostic performance of a 21-amino-acid-long peptide that spans TSSA-CL major antigenic determinants, which was similar to the performance of the previously validated glutathione S-transferase (GST)-TSSA-CL fusion molecule. Furthermore, the tools developed for the antigenic characterization of the TSSA antigen were also used to explore other potential diagnostic applications of the anti-TSSA humoral response in Chagasic patients. Overall, our present results provide additional insights into the antigenic structure of TSSA-CL and support this molecule as an excellent target for molecular intervention in Chagas disease. PMID:25589551

A highly sensitive nanoscale pH-sensor using Au nanoparticles linked by a multifunctional Raman-active reporter molecule.

PubMed

Lawson, Latevi S; Chan, James W; Huser, Thomas

2014-07-21

Chemical sensing on the nanoscale has been breaking new ground since the discovery of surface enhanced Raman scattering (SERS). For nanoparticles, controlled particle aggregation is necessary to achieve the largest SERS enhancements. Therefore, aggregating agents such as salts or linker molecules are used in conjunction with chemically sensitive reporters in order to develop robust environmentally sensitive SERS probes. While salt-induced colloidal nanosphere aggregates have produced robust SERS signals, their variability in aggregate size contributes significantly to poor SERS signal reproducibility, which can complicate their use in in vitro cellular studies. Such systems often also lack reproducibility in spectral measurements between different nanoparticle clusters. Preaggregation of colloids via linkers followed by surface functionalization with reporter molecules results in the linker occupying valuable SERS hotspot volume which could otherwise be utilized by additional reporter molecules. Ideally, both functionalities should be obtained from a single molecule. Here, we report the use of 3,5-dimercaptobenzoic acid, a single multifunctional molecule that creates SERS hotspots via the controlled aggregation of nanoparticles, and also reports pH values. We show that 3,5-dimercaptobenzoic acid bound to Au nanospheres results in an excellent pH nanoprobe, producing very robust, and highly reproducible SERS signals that can report pH across the entire physiological range with excellent pH resolution. To demonstrate the efficacy of our novel pH reporters, these probes were also used to image both the particle and pH distribution in the cytoplasm of human induced pluripotent stem cells (hiPSCs).

Nanomechanics of Yeast Surfaces Revealed by AFM

NASA Astrophysics Data System (ADS)

Dague, Etienne; Beaussart, Audrey; Alsteens, David

Despite the large and well-documented characterization of the microbial cell wall in terms of chemical composition, the determination of the mechanical properties of surface molecules in relation to their function remains a key challenge in cell biology.The emergence of powerful tools allowing molecular manipulations has already revolutionized our understanding of the surface properties of fungal cells. At the frontier between nanophysics and molecular biology, atomic force microscopy (AFM), and more specifically single-molecule force spectroscopy (SMFS), has strongly contributed to our current knowledge of the cell wall organization and nanomechanical properties. However, due to the complexity of the technique, measurements on live cells are still at their infancy.In this chapter, we describe the cell wall composition and recapitulate the principles of AFM as well as the main current methodologies used to perform AFM measurements on live cells, including sample immobilization and tip functionalization.The current status of the progress in probing nanomechanics of the yeast surface is illustrated through three recent breakthrough studies. Determination of the cell wall nanostructure and elasticity is presented through two examples: the mechanical response of mannoproteins from brewing yeasts and elasticity measurements on lacking polysaccharide mutant strains. Additionally, an elegant study on force-induced unfolding and clustering of adhesion proteins located at the cell surface is also presented.

Reversible Self-Assembly of Glutathione-Coated Gold Nanoparticle Clusters via pH-Tunable Interactions

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

Moaseri, Ehsan; Bollinger, Jonathan A.; Changalvaie, Behzad

In this study, nanoparticle (NP) clusters with diameters ranging from 20 to 100 nm are reversibly assembled from 5 nm gold (Au) primary particles coated with glutathione (GSH) in aqueous solution as a function of pH in the range of 5.4 to 3.8. As the pH is lowered, the GSH surface ligands become partially zwitterionic and form interparticle hydrogen bonds that drive the self-limited assembly of metastable clusters in <1 min. Whereas clusters up to 20 nm in size are stable against cluster–cluster aggregation for up to 1 day, clusters up to 80 nm in size can be stabilized overmore » this period via the addition of citrate to the solution in equal molarity with GSH molecules. The cluster diameter may be cycled reversibly by tuning pH to manipulate the colloidal interactions; however, modest background cluster–cluster aggregation occurs during cycling. Cluster sizes can be stabilized for at least 1 month via the addition of PEG-thiol as a grafted steric stabilizer, where PEG-grafted clusters dissociate back to starting primary NPs at pH 7 in fewer than 3 days. Whereas the presence of excess citrate has little effect on the initial size of the metastable clusters, it is necessary for both the cycling and dissociation to mediate the GSH–GSH hydrogen bonds. In conclusion, these metastable clusters exhibit significant characteristics of equilibrium self-limited assembly between primary particles and clusters on time scales where cluster–cluster aggregation is not present.« less

Reversible Self-Assembly of Glutathione-Coated Gold Nanoparticle Clusters via pH-Tunable Interactions

DOE PAGES

Moaseri, Ehsan; Bollinger, Jonathan A.; Changalvaie, Behzad; ...

2017-10-06

In this study, nanoparticle (NP) clusters with diameters ranging from 20 to 100 nm are reversibly assembled from 5 nm gold (Au) primary particles coated with glutathione (GSH) in aqueous solution as a function of pH in the range of 5.4 to 3.8. As the pH is lowered, the GSH surface ligands become partially zwitterionic and form interparticle hydrogen bonds that drive the self-limited assembly of metastable clusters in <1 min. Whereas clusters up to 20 nm in size are stable against cluster–cluster aggregation for up to 1 day, clusters up to 80 nm in size can be stabilized overmore » this period via the addition of citrate to the solution in equal molarity with GSH molecules. The cluster diameter may be cycled reversibly by tuning pH to manipulate the colloidal interactions; however, modest background cluster–cluster aggregation occurs during cycling. Cluster sizes can be stabilized for at least 1 month via the addition of PEG-thiol as a grafted steric stabilizer, where PEG-grafted clusters dissociate back to starting primary NPs at pH 7 in fewer than 3 days. Whereas the presence of excess citrate has little effect on the initial size of the metastable clusters, it is necessary for both the cycling and dissociation to mediate the GSH–GSH hydrogen bonds. In conclusion, these metastable clusters exhibit significant characteristics of equilibrium self-limited assembly between primary particles and clusters on time scales where cluster–cluster aggregation is not present.« less

Ion mobility spectrometry-mass spectrometry examination of the structures, stabilities, and extents of hydration of dimethylamine-sulfuric acid clusters.

PubMed

Thomas, Jikku M; He, Siqin; Larriba-Andaluz, Carlos; DePalma, Joseph W; Johnston, Murray V; Hogan, Christopher J

2016-08-17

We applied an atmospheric pressure differential mobility analyzer (DMA) coupled to a time-of-flight mass spectrometer to examine the stability, mass-mobility relationship, and extent of hydration of dimethylamine-sulfuric acid cluster ions, which are of relevance to nucleation in ambient air. Cluster ions were generated by electrospray ionization and were of the form: [H((CH3)2NH)x(H2SO4)y](+) and [(HSO4)((CH3)2NH)x(H2SO4)y](-), where 4 ≤ x ≤ 8, and 5 ≤ y ≤ 12. Under dry conditions, we find that positively charged cluster ions dissociated via loss of both multiple dimethylamine and sulfuric acid molecules after mobility analysis but prior to mass analysis, and few parent ions were detected in the mass spectrometer. Dissociation also occurred for negative ions, but to a lesser extent than for positive ions for the same mass spectrometer inlet conditions. Under humidified conditions (relative humidities up to 30% in the DMA), positively charged cluster ion dissociation in the mass spectrometer inlet was mitigated and occurred primarily by H2SO4 loss from ions containing excess acid molecules. DMA measurements were used to infer collision cross sections (CCSs) for all identifiable cluster ions. Stokes-Millikan equation and diffuse/inelastic gas molecule scattering predicted CCSs overestimate measured CCSs by more than 15%, while elastic-specular collision model predictions are in good agreement with measurements. Finally, cluster ion hydration was examined by monitoring changes in CCSs with increasing relative humidity. All examined cluster ions showed a modest amount of water molecule adsorption, with percentage increases in CCS smaller than 10%. The extent of hydration correlates directly with cluster ion acidity for positive ions.

Water-chromophore electron transfer determines the photochemistry of cytosine and cytidine.

PubMed

Szabla, Rafał; Kruse, Holger; Šponer, Jiří; Góra, Robert W

2017-07-21

Many of the UV-induced phenomena observed experimentally for aqueous cytidine were lacking the mechanistic interpretation for decades. These processes include the substantial population of the puzzling long-lived dark state, photohydration, cytidine to uridine conversion and oxazolidinone formation. Here, we present quantum-chemical simulations of excited-state spectra and potential energy surfaces of N1-methylcytosine clustered with two water molecules using the second-order approximate coupled cluster (CC2), complete active space with second-order perturbation theory (CASPT2), and multireference configuration interaction with single and double excitation (MR-CISD) methods. We argue that the assignment of the long-lived dark state to a singlet nπ* excitation involving water-chromophore electron transfer might serve as an explanation for the numerous experimental observations. While our simulated spectra for the state are in excellent agreement with experimentally acquired data, the electron-driven proton transfer process occurring on the surface may initiate the subsequent damage in the vibrationally hot ground state of the chromophore.

Combinatorial Broadening Mechanism of O-H Stretching Bands in H-Bonded Molecular Clusters

NASA Astrophysics Data System (ADS)

Pitsevich, G. A.; Doroshenko, I. Yu.; Pogorelov, V. E.; Pettersson, L. G. M.; Sablinskas, V.; Sapeshko, V. V.; Balevicius, V.

2016-07-01

A new mechanism for combinatorial broadening of donor-OH stretching-vibration absorption bands in molecular clusters with H-bonds is proposed. It enables the experimentally observed increase of the O-H stretching-vibration bandwidth with increasing number of molecules in H-bonded clusters to be explained. Knowledge of the half-width of the OH stretching-vibration absorption band in the dimer and the number of H-bonds in the analyzed cluster is suffi cient in the zeroth-order approximation to estimate the O-H stretching-absorption bands in clusters containing several molecules. Good agreement between the calculated and published experimental half-widths of the OH stretching-vibration absorption bands in MeOH and PrOH clusters was obtained using this approach.

Formation of Core-Shell Ethane-Silver Clusters in He Droplets.

PubMed

Loginov, Evgeny; Gomez, Luis F; Sartakov, Boris G; Vilesov, Andrey F

2017-08-17

Ethane core-silver shell clusters consisting of several thousand particles have been assembled in helium droplets upon capture of ethane molecules followed by Ag atoms. The composite clusters were studied via infrared laser spectroscopy in the range of the C-H stretching vibrations of ethane. The spectra reveal a splitting of the vibrational bands, which is ascribed to interaction with Ag. A rigorous analysis of band intensities for a varying number of trapped ethane molecules and Ag atoms indicates that the composite clusters consist of a core of ethane that is covered by relatively small Ag clusters. This metastable structure is stabilized due to fast dissipation in superfluid helium droplets of the cohesion energy of the clusters.

Fluctuating micro-heterogeneity in water-tert-butyl alcohol mixtures and lambda-type divergence of the mean cluster size with phase transition-like multiple anomalies

NASA Astrophysics Data System (ADS)

Banerjee, Saikat; Furtado, Jonathan; Bagchi, Biman

2014-05-01

Water-tert-butyl alcohol (TBA) binary mixture exhibits a large number of thermodynamic and dynamic anomalies. These anomalies are observed at surprisingly low TBA mole fraction, with xTBA ≈ 0.03-0.07. We demonstrate here that the origin of the anomalies lies in the local structural changes that occur due to self-aggregation of TBA molecules. We observe a percolation transition of the TBA molecules at xTBA ≈ 0.05. We note that "islands" of TBA clusters form even below this mole fraction, while a large spanning cluster emerges above that mole fraction. At this percolation threshold, we observe a lambda-type divergence in the fluctuation of the size of the largest TBA cluster, reminiscent of a critical point. Alongside, the structure of water is also perturbed, albeit weakly, by the aggregation of TBA molecules. There is a monotonic decrease in the tetrahedral order parameter of water, while the dipole moment correlation shows a weak nonlinearity. Interestingly, water molecules themselves exhibit a reverse percolation transition at higher TBA concentration, xTBA ≈ 0.45, where large spanning water clusters now break-up into small clusters. This is accompanied by significant divergence of the fluctuations in the size of largest water cluster. This second transition gives rise to another set of anomalies around. Both the percolation transitions can be regarded as manifestations of Janus effect at small molecular level.

Fluctuating micro-heterogeneity in water-tert-butyl alcohol mixtures and lambda-type divergence of the mean cluster size with phase transition-like multiple anomalies.

PubMed

Banerjee, Saikat; Furtado, Jonathan; Bagchi, Biman

2014-05-21

Water-tert-butyl alcohol (TBA) binary mixture exhibits a large number of thermodynamic and dynamic anomalies. These anomalies are observed at surprisingly low TBA mole fraction, with x(TBA) ≈ 0.03-0.07. We demonstrate here that the origin of the anomalies lies in the local structural changes that occur due to self-aggregation of TBA molecules. We observe a percolation transition of the TBA molecules at x(TBA) ≈ 0.05. We note that "islands" of TBA clusters form even below this mole fraction, while a large spanning cluster emerges above that mole fraction. At this percolation threshold, we observe a lambda-type divergence in the fluctuation of the size of the largest TBA cluster, reminiscent of a critical point. Alongside, the structure of water is also perturbed, albeit weakly, by the aggregation of TBA molecules. There is a monotonic decrease in the tetrahedral order parameter of water, while the dipole moment correlation shows a weak nonlinearity. Interestingly, water molecules themselves exhibit a reverse percolation transition at higher TBA concentration, x(TBA) ≈ 0.45, where large spanning water clusters now break-up into small clusters. This is accompanied by significant divergence of the fluctuations in the size of largest water cluster. This second transition gives rise to another set of anomalies around. Both the percolation transitions can be regarded as manifestations of Janus effect at small molecular level.

Comparative analysis of ArnCl2 (2 ? n ? 30) clusters taking into account molecular relaxation effects

NASA Astrophysics Data System (ADS)

Ferreira, G. G.; Borges, E.; Braga, J. P.; Belchior, J. C.

Cluster structures are discussed in a nonrigid analysis, using a modified minima search method based on stochastic processes and classical dynamics simulations. The relaxation process is taken into account considering the internal motion of the Cl2 molecule. Cluster structures are compared with previous works in which the Cl2 molecule is assumed to be rigid. The interactions are modeled using pair potentials: the Aziz and Lennard-Jones potentials for the Ar==Ar interaction, a Morse potential for the Cl==Cl interaction, and a fully spherical/anisotropic Morse-Spline-van der Waals (MSV) potential for the Ar==Cl interaction. As expected, all calculated energies are lower than those obtained in a rigid approximation; one reason may be attributed to the nonrigid contributions of the internal motion of the Cl2 molecule. Finally, the growing processes in molecular clusters are discussed, and it is pointed out that the growing mechanism can be affected due to the nonrigid initial conditions of smaller clusters such as ArnCl2 (n ? 4 or 5), which are seeds for higher-order clusters.

The quantum structure of anionic hydrogen clusters

NASA Astrophysics Data System (ADS)

Calvo, F.; Yurtsever, E.

2018-03-01

A flexible and polarizable interatomic potential has been developed to model hydrogen clusters interacting with one hydrogen anion, (H2)nH-, in a broad range of sizes n = 1-54 and parametrized against coupled cluster quantum chemical calculations. Using path-integral molecular dynamics simulations at 1 K initiated from the putative classical global minima, the equilibrium structures are found to generally rely on icosahedral shells with the hydrogen molecules pointing toward the anion, producing geometric magic numbers at sizes n = 12, 32, and 44 that are in agreement with recent mass spectrometry measurements. The energetic stability of the clusters is also connected with the extent of vibrational delocalization, measured here by the fluctuations among inherent structures hidden in the vibrational wave function. As the clusters grow, the outer molecules become increasingly free to rotate, and strong finite size effects are also found between magic numbers, associated with more prominent vibrational delocalization. The effective icosahedral structure of the 44-molecule cluster is found to originate from quantum nuclear effects as well, the classical structure showing no particular symmetry.

Tailoring oxide properties: An impact on adsorption characteristics of molecules and metals

NASA Astrophysics Data System (ADS)

Honkala, Karoliina

2014-12-01

Both density functional theory calculations and numerous experimental studies demonstrate a variety of unique features in metal supported oxide films and transition metal doped simple oxides, which are markedly different from their unmodified counterparts. This review highlights, from the computational perspective, recent literature on the properties of the above mentioned surfaces and how they adsorb and activate different species, support metal aggregates, and even catalyse reactions. The adsorption of Au atoms and clusters on metal-supported MgO films are reviewed together with the cluster's theoretically predicted ability to activate and dissociate O2 at the Au-MgO(100)/Ag(100) interface, as well as the impact of an interface vacancy to the binding of an Au atom. In contrast to a bulk MgO surface, an Au atom binds strongly on a metal-supported ultra-thin MgO film and becomes negatively charged. Similarly, Au clusters bind strongly on a supported MgO(100) film and are negatively charged favouring 2D planar structures. The adsorption of other metal atoms is briefly considered and compared to that of Au. Existing computational literature of adsorption and reactivity of simple molecules including O2, CO, NO2, and H2O on mainly metal-supported MgO(100) films is discussed. Chemical reactions such as CO oxidation and O2 dissociation are discussed on the bare thin MgO film and on selected Au clusters supported on MgO(100)/metal surfaces. The Au atoms at the perimeter of the cluster are responsible for catalytic activity and calculations predict that they facilitate dissociative adsorption of oxygen even at ambient conditions. The interaction of H2O with a flat and stepped Ag-supported MgO film is summarized and compared to bulk MgO. The computational results highlight spontaneous dissociation on MgO steps. Furthermore, the impact of water coverage on adsorption and dissociation is addressed. The modifications, such as oxygen vacancies and dopants, at the oxide-metal interface and their effect on the adsorption characteristics of water and Au are summarized. Finally, more limited computational literature on transition metal (TM) doped CaO(100) and MgO(100) surfaces is presented. Again, Au is used as a probe species. Similar to metal-supported MgO films, Au binds more strongly than on undoped CaO(100) and becomes negatively charged. The discussion focuses on rationalization of Au adsorption with the help of Born-Haber cycle, which reveals that the so-called redox energy including the electron transfer from the dopant to the Au atom together with the simultaneous structural relaxation of lattice atoms is responsible for enhanced binding. In addition, adsorption energy dependence on the position and type of the dopant is summarized.

Redox Behavior of the S-Adenosylmethionine (SAM)-Binding Fe-S Cluster in Methylthiotransferase RimO, toward Understanding Dual SAM Activity.

PubMed

Molle, Thibaut; Moreau, Yohann; Clemancey, Martin; Forouhar, Farhad; Ravanat, Jean-Luc; Duraffourg, Nicolas; Fourmond, Vincent; Latour, Jean-Marc; Gambarelli, Serge; Mulliez, Etienne; Atta, Mohamed

2016-10-18

RimO, a radical-S-adenosylmethionine (SAM) enzyme, catalyzes the specific C 3 methylthiolation of the D89 residue in the ribosomal S 12 protein. Two intact iron-sulfur clusters and two SAM cofactors both are required for catalysis. By using electron paramagnetic resonance, Mössbauer spectroscopies, and site-directed mutagenesis, we show how two SAM molecules sequentially bind to the unique iron site of the radical-SAM cluster for two distinct chemical reactions in RimO. Our data establish that the two SAM molecules bind the radical-SAM cluster to the unique iron site, and spectroscopic evidence obtained under strongly reducing conditions supports a mechanism in which the first molecule of SAM causes the reoxidation of the reduced radical-SAM cluster, impeding reductive cleavage of SAM to occur and allowing SAM to methylate a HS - ligand bound to the additional cluster. Furthermore, by using density functional theory-based methods, we provide a description of the reaction mechanism that predicts the attack of the carbon radical substrate on the methylthio group attached to the additional [4Fe-4S] cluster.

Computational Study of Interstellar Glycine Formation Occurring at Radical Surfaces of Water-ice Dust Particles

NASA Astrophysics Data System (ADS)

Rimola, Albert; Sodupe, Mariona; Ugliengo, Piero

2012-07-01

Glycine is the simplest amino acid, and due to the significant astrobiological implications that suppose its detection, the search for it in the interstellar medium (ISM), meteorites, and comets is intensively investigated. In the present work, quantum mechanical calculations based on density functional theory have been used to model the glycine formation on water-ice clusters present in the ISM. The removal of either one H atom or one electron from the water-ice cluster has been considered to simulate the effect of photolytic radiation and of ionizing particles, respectively, which lead to the formation of OH• radical and H3O+ surface defects. The coupling of incoming CO molecules with the surface OH• radicals on the ice clusters yields the formation of the COOH• radicals via ZPE-corrected energy barriers and reaction energies of about 4-5 kcal mol-1 and -22 kcal mol-1, respectively. The COOH• radicals couple with incoming NH=CH2 molecules (experimentally detected in the ISM) to form the NHCH2COOH• radical glycine through energy barriers of 12 kcal mol-1, exceedingly high at ISM cryogenic temperatures. Nonetheless, when H3O+ is present, one proton may be barrierless transferred to NH=CH2 to give NH2=CH2 +. This latter may react with the COOH• radical to give the NH2CH2COOH+• glycine radical cation which can then be transformed into the NH2CHC(OH)2 +• species (the most stable form of glycine in its radical cation state) or into the NH2CHCOOH• neutral radical glycine. Estimated rate constants of these events suggest that they are kinetically feasible at temperatures of 100-200 K, which indicate that their occurrence may take place in hot molecular cores or in comets exposed to warmer regions of solar systems. Present results provide quantum chemical evidence that defects formed on water ices due to the harsh-physical conditions of the ISM may trigger reactions of cosmochemical interest. The relevance of surface H3O+ ions to facilitate chemical processes by proton transfer (i.e., acting as acidic catalysts) is highlighted, and plausible ways of their formation at the water-ice surface in the ISM are also discussed.

Electron-induced hydrogen loss in uracil in a water cluster environment

NASA Astrophysics Data System (ADS)

Smyth, M.; Kohanoff, J.; Fabrikant, I. I.

2014-05-01

Low-energy electron-impact hydrogen loss due to dissociative electron attachment (DEA) to the uracil and thymine molecules in a water cluster environment is investigated theoretically. Only the A'-resonance contribution, describing the near-threshold behavior of DEA, is incorporated. Calculations are based on the nonlocal complex potential theory and the multiple scattering theory, and are performed for a model target with basic properties of uracil and thymine, surrounded by five water molecules. The DEA cross section is strongly enhanced when the attaching molecule is embedded in a water cluster. This growth is due to two effects: the increase of the resonance lifetime and the negative shift in the resonance position due to interaction of the intermediate negative ion with the surrounding water molecules. A similar effect was earlier found in DEA to chlorofluorocarbons.

Water penetration/accommodation and phase behaviour of the neutral Langmuir monolayer at the air/water interface probed with sum frequency generation vibrational spectroscopy (SFG-VS).

PubMed

Zhang, Zhen; Zheng, De-Sheng; Guo, Yuan; Wang, Hong-Fei

2009-02-14

A strong and broad hydrogen bonded O-H band around 3520 cm(-1) is observed in the insoluble monolayer of the neutral liquid crystal molecules of 4''-n-pentyl-4-p-cyanobiphenyl (5CB) and 4''-n-octyl-4-p-cyanobiphenyl (8CB) throughout the whole surface density range, but not in the 4-pentyl-4'-cyanoterphenyl (5CT) monolayer, at the air/water interface. This novel spectral feature suggests the existence of an oriented water cluster species which has penetrated or accommodated into the Langmuir monolayer of the 8CB and 5CB molecules. This finding provided a molecular level mechanism for the stark difference in the phase behaviour between the CB and CT insoluble Langmuir monolayers at the air/water interface. It also calls for attention to the details of the specific water-surface interaction in mediating the structure and the phase behaviour of the molecular assemblies at the heterogeneous aqueous interfaces.

Adsorption of formamide over pristine and Al-doped boron nitride nanosheets: A dispersion-corrected DFT study.

PubMed

Esrafili, Mehdi D; Mousavian, Parisasadat; Arjomandi Rad, Farzad

2018-06-01

Using the dispersion-corrected DFT calculations, different adsorption modes of formamide molecule are studied over the pristine and Al-doped boron nitride nanosheets (BNNS). It is found that the interaction between the Al atom and its neighboring N atoms in the Al-doped BNNS is very strong, which would hinder the dispersion and clustering of the Al atoms over the BNNS surface. Unlike the pristine nanosheet, the electronic properties of Al-doped BNNS are very sensitive to the formamide adsorption. The adsorption energies of formamide over the Al-doped sheet are in the range of -0.93 to -1.85 eV, which indicates the quite strong interaction of this molecule with the surface. Moreover, the dehydrogenation of formamide over the Al-doped BNNS is examined. According to our results, the N-H bond scission of formamide is more energetically favorable than the C-H one. Copyright © 2018 Elsevier Inc. All rights reserved.

The role of defective silica surfaces in exogenous delivery of prebiotic compounds: clues from first principles calculations.

PubMed

Rimola, Albert; Ugliengo, Piero

2009-04-14

The reaction of glycine (Gly) with a strained (SiO)(2) four-membered ring defect (D2) at the surface of an interstellar silica grain dust has been studied at ONIOM2[B3LYP/6-31+G(d,p):MNDO] level within a cluster approach in the context of hypothetical reactions occurring in the interstellar medium. The D2 opens up exothermically for reaction with Gly (Delta(r)U(0)=-26.3 kcal mol(-1)) to give a surface mixed anhydride S(surf)-O-C([double bond, length as m-dash]O)-CH(2)NH(2) as a product. The reaction barriers, DeltaU( not equal)(0), are 0.1 and 10.4 kcal mol(-1) for reactive channels involving COOH and NH(2) as attacking groups, respectively. Calculations show the surface mixed anhydride to be rather stable under the action of interstellar processes, such as reactions with isolated H(2)O and NH(3) molecules or the exposure to cosmic rays and UV radiation. The hydrolysis of the surface mixed anhydride to release again Gly was modelled by microsolvation (from 1 to 4 H(2)O molecules) mimicking what could have happened to the interstellar dust after seeding the primordial ocean in the early Earth. Results for these calculations show that the reaction is exergonic and activated, the Delta(r)G(298) becoming more negative and the DeltaG( not equal)(298) being dramatically reduced as a function of increasing number of H(2)O molecules. The present results are relevant because they show that defects present at interstellar dust surfaces could have played a significant role in capturing, protecting and delivering essential prebiotic compounds on the early Earth.

Water clusters in amorphous pharmaceuticals.

PubMed

Authelin, Jean-Rene; MacKenzie, Alan P; Rasmussen, Don H; Shalaev, Evgenyi Y

2014-09-01

Amorphous materials, although lacking the long-range translational and rotational order of crystalline and liquid crystalline materials, possess certain local (short-range) structure. This paper reviews the distribution of one particular component present in all amorphous pharmaceuticals, that is, water. Based on the current understanding of the structure of water, water molecules can exist in either unclustered form or as aggregates (clusters) of different sizes and geometries. Water clusters are reported in a range of amorphous systems including carbohydrates and their aqueous solutions, synthetic polymers, and proteins. Evidence of water clustering is obtained by various methods that include neutron and X-ray scattering, molecular dynamics simulation, water sorption isotherm, concentration dependence of the calorimetric Tg , dielectric relaxation, and nuclear magnetic resonance. A review of the published data suggests that clustering depends on water concentration, with unclustered water molecules existing at low water contents, whereas clusters form at intermediate water contents. The transition from water clusters to unclustered water molecules can be expected to change water dependence of pharmaceutical properties, such as rates of degradation. We conclude that a mechanistic understanding of the impact of water on the stability of amorphous pharmaceuticals would require systematic studies of water distribution and clustering, while such investigations are lacking. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

Adsorption of small molecules on the [Zn-Zn]2+ linkage in zeolite. A DFT study of ferrierite

NASA Astrophysics Data System (ADS)

Benco, Lubomir

2017-02-01

In zeolites monovalent Zn(I) forms a sub-nano particles [Zn-Zn]2+ stabilized in rings of the zeolite framework, which exhibit interesting catalytic properties. This work reports on adsorption properties of [Zn-Zn]2+ particles in zeolite ferrierite investigated for a set of probing diatomic (N2, O2, H2, CO, NO) and triatomic (CO2, N2O, NO2, H2O) molecules using dispersion-corrected DFT. Three [Zn-Zn]2+ sites are compared differing in the location and stability. On all sites molecules form physisorbed clusters with the molecule connected on-top of the Zn-Zn linkage. In physisorbed clusters adsorption induces only slight change of bonding and the geometry of the Zn-Zn linkage. Some molecules can form stable chemisorbed clusters in which the molecule is integrated between two Zn+ cations. The sandwich-like chemisorption causes pronounced changes of bonding and can lead to the transfer of the electron density between two Zn+ cations and to a change of the oxidation state. The knowledge of bonding of small molecules can help understanding of the mechanism of conversion reactions catalyzed by sub-nano [Zn-Zn] particles.

Nanoscale patterning of STIM1 and Orai1 during store-operated Ca2+ entry.

PubMed

Perni, Stefano; Dynes, Joseph L; Yeromin, Andriy V; Cahalan, Michael D; Franzini-Armstrong, Clara

2015-10-06

Stromal interacting molecule (STIM) and Orai proteins constitute the core machinery of store-operated calcium entry. We used transmission and freeze-fracture electron microscopy to visualize STIM1 and Orai1 at endoplasmic reticulum (ER)-plasma membrane (PM) junctions in HEK 293 cells. Compared with control cells, thin sections of STIM1-transfected cells possessed far more ER elements, which took the form of complex stackable cisternae and labyrinthine structures adjoining the PM at junctional couplings (JCs). JC formation required STIM1 expression but not store depletion, induced here by thapsigargin (TG). Extended molecules, indicative of STIM1, decorated the cytoplasmic surface of ER, bridged a 12-nm ER-PM gap, and showed clear rearrangement into small clusters following TG treatment. Freeze-fracture replicas of the PM of Orai1-transfected cells showed extensive domains packed with characteristic "particles"; TG treatment led to aggregation of these particles into sharply delimited "puncta" positioned upon raised membrane subdomains. The size and spacing of Orai1 channels were consistent with the Orai crystal structure, and stoichiometry was unchanged by store depletion, coexpression with STIM1, or an Orai1 mutation (L273D) affecting STIM1 association. Although the arrangement of Orai1 channels in puncta was substantially unstructured, a portion of channels were spaced at ∼15 nm. Monte Carlo analysis supported a nonrandom distribution for a portion of channels spaced at ∼15 nm. These images offer dramatic, direct views of STIM1 aggregation and Orai1 clustering in store-depleted cells and provide evidence for the interaction of a single Orai1 channel with small clusters of STIM1 molecules.

Nanoscale patterning of STIM1 and Orai1 during store-operated Ca2+ entry

PubMed Central

Perni, Stefano; Dynes, Joseph L.; Yeromin, Andriy V.; Cahalan, Michael D.; Franzini-Armstrong, Clara

2015-01-01

Stromal interacting molecule (STIM) and Orai proteins constitute the core machinery of store-operated calcium entry. We used transmission and freeze–fracture electron microscopy to visualize STIM1 and Orai1 at endoplasmic reticulum (ER)–plasma membrane (PM) junctions in HEK 293 cells. Compared with control cells, thin sections of STIM1-transfected cells possessed far more ER elements, which took the form of complex stackable cisternae and labyrinthine structures adjoining the PM at junctional couplings (JCs). JC formation required STIM1 expression but not store depletion, induced here by thapsigargin (TG). Extended molecules, indicative of STIM1, decorated the cytoplasmic surface of ER, bridged a 12-nm ER-PM gap, and showed clear rearrangement into small clusters following TG treatment. Freeze–fracture replicas of the PM of Orai1-transfected cells showed extensive domains packed with characteristic “particles”; TG treatment led to aggregation of these particles into sharply delimited “puncta” positioned upon raised membrane subdomains. The size and spacing of Orai1 channels were consistent with the Orai crystal structure, and stoichiometry was unchanged by store depletion, coexpression with STIM1, or an Orai1 mutation (L273D) affecting STIM1 association. Although the arrangement of Orai1 channels in puncta was substantially unstructured, a portion of channels were spaced at ∼15 nm. Monte Carlo analysis supported a nonrandom distribution for a portion of channels spaced at ∼15 nm. These images offer dramatic, direct views of STIM1 aggregation and Orai1 clustering in store-depleted cells and provide evidence for the interaction of a single Orai1 channel with small clusters of STIM1 molecules. PMID:26351694

Sink or Swim: Ions and Organics at the Ice-Air Interface.

PubMed

Hudait, Arpa; Allen, Michael T; Molinero, Valeria

2017-07-26

The ice-air interface is an important locus of environmental chemical reactions. The structure and dynamics of the ice surface impact the uptake of trace gases and kinetics of reactions in the atmosphere and snowpack. At tropospheric temperatures, the ice surface is partially premelted. Experiments indicate that ions increase the liquidity of the ice surface but hydrophilic organics do not. However, it is not yet known the extent of the perturbation solutes induce at the ice surface and what is the role of the disordered liquid-like layer in modulating the interaction between solutes and their mobility and aggregation at the ice surface. Here we use large-scale molecular simulations to investigate the effect of ions and glyoxal, one of the most abundant oxygenated volatile organic compounds in the atmosphere, on the structure, dynamics, and solvation properties of the ice surface. We find that the premelted surface of ice has unique solvation properties, different from those of liquid water. The increase in surface liquidity resulting from the hydration of ions leads to a water-mediated attraction of ions at the ice surface. Glyoxal molecules, on the other hand, perturb only slightly the surface of ice and do not experience water-driven attraction. They nonetheless accumulate as dry agglomerates at the ice surface, driven by direct interactions between the organic molecules. The enhanced attraction and clustering of ions and organics at the ice surface may play a significant role in modulating the mechanism and rate of heterogeneous chemical reactions occurring at the surface of atmospheric ice particles.

Adsorption geometry and core excitation spectra of three phenylpropene isomers on Cu(111)

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

Kolczewski, C.; Williams, F. J.; Cropley, R. L.

Theoretical C 1s near edge x-ray absorption fine structure (NEXAFS) spectra for the C{sub 9}H{sub 10} isomers trans-methylstyrene, {alpha}-methylstyrene, and allylbenzene in gas phase and adsorbed at Cu(111) surfaces have been obtained from density functional theory calculations where adsorbate geometries were determined by corresponding total energy optimizations. The three species show characteristic differences in widths and peak shapes of the lowest C 1s{yields}{pi}* transitions which are explained by different coupling of the {pi}-electron system of the C{sub 6} ring with that of the side chain in the molecules as well as by the existence of nonequivalent carbon centers. The adsorbedmore » molecules bind only weakly with the substrate which makes the use of theoretical NEXAFS spectra of the oriented free molecules meaningful for an interpretation of experimental angle-resolved NEXAFS spectra of the adsorbate systems obtained in this work. However, a detailed quantitative account of relative peak intensities requires theoretical angle-resolved NEXAFS spectra of the complete adsorbate systems which have been evaluated within the surface cluster approach. The comparison with experiment yields almost perfect agreement and confirms the reliability of the calculated equilibrium geometries of the adsorbates. This can help to explain observed differences in the catalytic epoxidation of the three molecules on Cu(111) based on purely geometric considerations.« less

Absolute single-ion solvation free energy scale in methanol determined by the lithium cluster-continuum approach.

PubMed

Pliego, Josefredo R; Miguel, Elizabeth L M

2013-05-02

Absolute solvation free energy of the lithium cation in methanol was calculated by the cluster-continuum quasichemical theory of solvation. Clusters with up to five methanol molecules were investigated using X3LYP, MP2, and MP4 methods with DZVP, 6-311+G(2df,2p), TZVPP+diff, and QZVPP+diff basis sets and including the cluster solvation through the PCM and SMD continuum models. Our calculations have determined a value of -118.1 kcal mol(-1) for the solvation free energy of the lithium, in close agreement with a value of -116.6 kcal mol(-1) consistent with the TATB assumption. Using data of solvation and transfer free energy of a pair of ions, electrode potentials and pKa, we have obtained the solvation free energy of 25 ions in methanol. Our analysis leads to a value of -253.6 kcal mol(-1) for the solvation free energy of the proton, which can be compared with the value of -263.5 kcal mol(-1) obtained by Kelly et al. using the cluster pair approximation. Considering that this difference is due to the methanol surface potential, we have estimated that it corresponds to -0.429 V.

Flow-induced detachment of red blood cells adhering to surfaces by specific antigen-antibody bonds.

PubMed

Xia, Z; Goldsmith, H L; van de Ven, T G

1994-04-01

Fixed spherical swollen human red blood cells of blood type B adhering on a glass surface through antigen-antibody bonds to monoclonal mouse antihuman IgM, adsorbed or covalently linked on the surface, were detached by known hydrodynamic forces created in an impinging jet. The dynamic process of detachment of the specifically bound cells was recorded and analyzed. The fraction of adherent cells remaining on the surface decreased with increasing hydrodynamic force. For an IgM coverage of 0.26%, a tangential force on the order of 100 pN was able to detach almost all of the cells from the surface within 20 min. After a given time of exposure to hydrodynamic force, the fraction of adherent cells remaining increased with time, reflecting an increase in adhesion strength. The characteristic time for effective aging was approximately 4 h. Results from experiments in which the adsorbed antibody molecules were immobilized through covalent coupling and from evanescent wave light scattering of adherent cells, imply that deformation of red cells at the contact area was the principal cause for aging, rather than local clustering of the antibody through surface diffusion. Experiments with latex beads specifically bound to red blood cells suggest that, instead of breaking the antigen-antibody bonds, antigen molecules were extracted from the cell membrane during detachment.

Chemical structural analysis of diamondlike carbon films: II. Raman analysis

NASA Astrophysics Data System (ADS)

Takabayashi, Susumu; Ješko, Radek; Shinohara, Masanori; Hayashi, Hiroyuki; Sugimoto, Rintaro; Ogawa, Shuichi; Takakuwa, Yuji

2018-02-01

The chemical structure of diamondlike carbon (DLC) films, synthesized by photoemission-assisted glow discharge, has been analyzed by Raman spectroscopy. Raman analysis in conjunction with the sp2 cluster model clarified the film structure. The sp2 clusters in DLC films synthesized at low temperature preferred various aliphatic structures. Sufficient argon-ion assist allowed for formation of less strained DLC films containing large amounts of hydrogen. As the synthesis temperature was increased, thermal desorption of hydrogen left carbon dangling bonds with active unpaired electrons in the films, and the reactions that followed created strained films containing aromatic sp2 clusters. In parallel, the desorption of methane molecules from the growing surface by chemisorption of hydrogen radicals prevented the action of argon ions, promoting internal strain of the films. However, in synthesis at very high temperature, where sp2 clusters are sufficiently dominant, the strain was dissolved gradually. In contrast, the DLC films synthesized at low temperature were more stable than other films synthesized at the same temperature because of stable hydrogen-carbon bonds in the films.

A density functional study of second-row dicarbides C2X (X = Na-Cl) with carbon monosulfide molecule: molecular structure and bonding mechanism

NASA Astrophysics Data System (ADS)

Parida, Saroj K.; Sahu, Sridhar

2018-05-01

In present work, a systematic study regarding molecular structure, and bonding mechanism of carbon monosulfide (CS) on second-row dicarbides C2X with (X = Na-Cl) has been investigated within the framework of density functional theory (DFT). In presence of carbon monosulfide molecule, the structures of C2Na, C2Mg, C2Al, and C2Si are found be changed from cyclic to linear, whereas geometries of C2P, C2S, and C2Cl clusters are almost remain unchanged. Interestingly, the bare carbon monosulfide molecule is attached with carbon site of bare C2X clusters rather than the second-row elements (X = Na-Cl). Furthermore, the nature of bonding in C2XCS clusters has been studiedthrough Bader's topological analysis of the electron charge density distribution ρ(r), Laplacian ∇2 ρ(r) and total energy density H BCP at the bond critical points (BCPs) of the clusters within the framework of the atoms in molecules theory (AIM). In C2XCS clusters, electron density at the bond critical point ρ(r) > 0.30 a.u. with negative values of Laplacian ∇2 ρ(r) indicates shared-kind of interactions between both the carbon atoms of C2X and CS molecule. In addition, we also analyze IR spectra that could assist for the experimental detection.

Infrared spectroscopy of hydrated naphthalene cluster anions.

PubMed

Knurr, Benjamin J; Adams, Christopher L; Weber, J Mathias

2012-09-14

We present infrared spectra of mass-selected C(10)H(8)(-)·(H(2)O)(n)·Ar(m) cluster anions (n = 1-6) obtained by Ar predissociation spectroscopy. The experimental spectra are compared with predicted spectra from density functional theory calculations. The OH groups of the water ligands are involved in H-bonds to other water molecules or to the π system of the naphthalene anion, which accommodates the excess electron. The interactions in the water network are generally found to be more important than those between water molecules and the ion. For 2 ≤ n ≤ 4 the water molecules form single layer water networks on one side of the naphthalene anion, while for n = 5 and 6, cage and multilayer structures become more energetically favorable. For cluster sizes with more than 3 water molecules, multiple conformers are likely to be responsible for the experimental spectra.

[Basic understanding of the HLA system in allogeneic hematopoietic cell transplantation].

PubMed

Ichinohe, Tatsuo

2015-10-01

Human immune responses are principally characterized by the human leukocyte antigen (HLA) system, a diverse set of cell surface molecules encoded by the major histocompatibility complex gene cluster on the short arm of chromosome 6. Among various members of the HLA family, the best characterized are the classic highly polymorphic class I and class II molecules that are responsible for antigen presentation to T cells and regulation of NK cell functions. In allogeneic hematopoietic cell transplantation, sophisticated approaches to donor-recipient allele-level matching at 3 class I (HLA-A/B/C) and 3 class II (HLA-DRB1/DQB1/DPB1) loci have been proven to lower the risk of immunologic complications such as graft failure and graft-versus-host disease, and possibly to confer effective graft-versus-malignancy effects. Future areas of research include clarifying the role of relatively non-polymorphic non-classical HLA molecules (HLA-E/F/G, HLA-DM/DO) and polymorphic/non-polymorphic class I-related molecules (MICA, MICB, HFE, MR1, CD1, FcRn) in the immune regulation that follows hematopoietic cell transplantation.

CO2 Cluster Ion Beam, an Alternative Projectile for Secondary Ion Mass Spectrometry.

PubMed

Tian, Hua; Maciążek, Dawid; Postawa, Zbigniew; Garrison, Barbara J; Winograd, Nicholas

2016-09-01

The emergence of argon-based gas cluster ion beams for SIMS experiments opens new possibilities for molecular depth profiling and 3D chemical imaging. These beams generally leave less surface chemical damage and yield mass spectra with reduced fragmentation compared with smaller cluster projectiles. For nanoscale bioimaging applications, however, limited sensitivity due to low ionization probability and technical challenges of beam focusing remain problematic. The use of gas cluster ion beams based upon systems other than argon offer an opportunity to resolve these difficulties. Here we report on the prospects of employing CO2 as a simple alternative to argon. Ionization efficiency, chemical damage, sputter rate, and beam focus are investigated on model compounds using a series of CO2 and Ar cluster projectiles (cluster size 1000-5000) with the same mass. The results show that the two projectiles are very similar in each of these aspects. Computer simulations comparing the impact of Ar2000 and (CO2)2000 on an organic target also confirm that the CO2 molecules in the cluster projectile remain intact, acting as a single particle of m/z 44. The imaging resolution employing CO2 cluster projectiles is improved by more than a factor of two. The advantage of CO2 versus Ar is also related to the increased stability which, in addition, facilitates the operation of the gas cluster ion beams (GCIB) system at lower backing pressure. Graphical Abstract ᅟ.

Three-dimensional structural modelling and calculation of electrostatic potentials of HLA Bw4 and Bw6 epitopes to explain the molecular basis for alloantibody binding: toward predicting HLA antigenicity and immunogenicity.

PubMed

Mallon, Dermot H; Bradley, J Andrew; Winn, Peter J; Taylor, Craig J; Kosmoliaptsis, Vasilis

2015-02-01

We have previously shown that qualitative assessment of surface electrostatic potential of HLA class I molecules helps explain serological patterns of alloantibody binding. We have now used a novel computational approach to quantitate differences in surface electrostatic potential of HLA B-cell epitopes and applied this to explain HLA Bw4 and Bw6 antigenicity. Protein structure models of HLA class I alleles expressing either the Bw4 or Bw6 epitope (defined by sequence motifs at positions 77 to 83) were generated using comparative structure prediction. The electrostatic potential in 3-dimensional space encompassing the Bw4/Bw6 epitope was computed by solving the Poisson-Boltzmann equation and quantitatively compared in a pairwise, all-versus-all fashion to produce distance matrices that cluster epitopes with similar electrostatics properties. Quantitative comparison of surface electrostatic potential at the carboxyl terminal of the α1-helix of HLA class I alleles, corresponding to amino acid sequence motif 77 to 83, produced clustering of HLA molecules in 3 principal groups according to Bw4 or Bw6 epitope expression. Remarkably, quantitative differences in electrostatic potential reflected known patterns of serological reactivity better than Bw4/Bw6 amino acid sequence motifs. Quantitative assessment of epitope electrostatic potential allowed the impact of known amino acid substitutions (HLA-B*07:02 R79G, R82L, G83R) that are critical for antibody binding to be predicted. We describe a novel approach for quantitating differences in HLA B-cell epitope electrostatic potential. Proof of principle is provided that this approach enables better assessment of HLA epitope antigenicity than amino acid sequence data alone, and it may allow prediction of HLA immunogenicity.

Size and Site Dependence of the Catalytic Activity of Iridium Clusters toward Ethane Dehydrogenation.

PubMed

Ge, Yingbin; Jiang, Hao; Kato, Russell; Gummagatta, Prasuna

2016-12-01

This research focuses on optimizing transition metal nanocatalyst immobilization and activity to enhance ethane dehydrogenation. Ethane dehydrogenation, catalyzed by thermally stable Ir n (n = 8, 12, 18) atomic clusters that exhibit a cuboid structure, was studied using the B3LYP method with triple-ζ basis sets. Relativistic effects and dispersion corrections were included in the calculations. In the dehydrogenation reaction Ir n + C 2 H 6 → H-Ir n -C 2 H 5 → (H) 2 -Ir n -C 2 H 4 , the first H-elimination is the rate-limiting step, primarily because the reaction releases sufficient heat to facilitate the second H-elimination. The catalytic activity of the Ir clusters strongly depends on the Ir cluster size and the specific catalytic site. Cubic Ir 8 is the least reactive toward H-elimination in ethane: Ir 8 + C 2 H 6 → H-Ir 8 -C 2 H 5 has a large (65 kJ/mol) energy barrier, whereas Ir 12 (3 × 2 × 2 cuboid) and Ir 18 (3 × 3 × 2 cuboid) lower this energy barrier to 22 and 3 kJ/mol, respectively. The site dependence is as prominent as the size effect. For example, the energy barrier for the Ir 18 + C 2 H 6 → H-Ir 18 -C 2 H 5 reaction is 3, 48, and 71 kJ/mol at the corner, edge, or face-center sites of the Ir 18 cuboid, respectively. Energy release due to Ir cluster insertion into an ethane C-H bond facilitates hydrogen migration on the Ir cluster surface, and the second H-elimination of ethane. In an oxygen-rich environment, oxygen molecules may be absorbed on the Ir cluster surface. The oxygen atoms bonded to the Ir cluster surface may slightly increase the energy barrier for H-elimination in ethane. However, the adsorption of oxygen and its reaction with H atoms on the Ir cluster releases sufficient heat to yield an overall thermodynamically favored reaction: Ir n + C 2 H 6 + 1 / 2 O 2 → Ir n + C 2 H 4 + H 2 O. These results will be useful toward reducing the energy cost of ethane dehydrogenation in industry.

Screening molecular associations with lipid membranes using natural abundance 13C cross-polarization magic-angle spinning NMR and principal component analysis.

PubMed

Middleton, David A; Hughes, Eleri; Madine, Jillian

2004-08-11

We describe an NMR approach for detecting the interactions between phospholipid membranes and proteins, peptides, or small molecules. First, 1H-13C dipolar coupling profiles are obtained from hydrated lipid samples at natural isotope abundance using cross-polarization magic-angle spinning NMR methods. Principal component analysis of dipolar coupling profiles for synthetic lipid membranes in the presence of a range of biologically active additives reveals clusters that relate to different modes of interaction of the additives with the lipid bilayer. Finally, by representing profiles from multiple samples in the form of contour plots, it is possible to reveal statistically significant changes in dipolar couplings, which reflect perturbations in the lipid molecules at the membrane surface or within the hydrophobic interior.

Water transport and clustering behavior in homopolymer and graft copolymer polylactide

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

Du, An; Koo, Donghun; Theryo, Grayce

2015-02-19

Polylactide is a bio-based and biodegradable polymer well-known for its renewable origins. Water sorption and clustering behavior in both a homopolymer polylactide and a graft copolymer of polylactide was studied using the quartz crystal microbalance/heat conduction calorimetry (QCM/HCC) technique. The graft copolymer, poly(1,5-cyclooctadiene-co-5-norbornene-2-methanol-graft-D,L-lactide), contained polylactide chains (95 wt.%) grafted onto a hydrophobic rubbery backbone (5 wt.%). Clustering is an important phenomenon in the study of water transport properties in polymers since the presence of water clusters can affect the water diffusivity. The HCC method using the thermal power signals and Van't Hoff's law were both employed to estimate the watermore » sorption enthalpy. Sorption enthalpy of water in both polymers was determined to be approximately -40 kJ/mol for all water activity levels. Zimm-Lundberg analysis showed that water clusters start to form at a water activity of 0.4. The engaged species induced clustering (ENSIC) model was used to curve fit sorption isotherms and showed that the affinity among water molecules is higher than that between water molecules and polymer chains. All the methods used indicate that clustering of water molecules exists in both polymers.« less

Photoionization cross section by Stieltjes imaging applied to coupled cluster Lanczos pseudo-spectra

NASA Astrophysics Data System (ADS)

Cukras, Janusz; Coriani, Sonia; Decleva, Piero; Christiansen, Ove; Norman, Patrick

2013-09-01

A recently implemented asymmetric Lanczos algorithm for computing (complex) linear response functions within the coupled cluster singles (CCS), coupled cluster singles and iterative approximate doubles (CC2), and coupled cluster singles and doubles (CCSD) is coupled to a Stieltjes imaging technique in order to describe the photoionization cross section of atoms and molecules, in the spirit of a similar procedure recently proposed by Averbukh and co-workers within the Algebraic Diagrammatic Construction approach. Pilot results are reported for the atoms He, Ne, and Ar and for the molecules H2, H2O, NH3, HF, CO, and CO2.

Photoionization cross section by Stieltjes imaging applied to coupled cluster Lanczos pseudo-spectra.

PubMed

Cukras, Janusz; Coriani, Sonia; Decleva, Piero; Christiansen, Ove; Norman, Patrick

2013-09-07

A recently implemented asymmetric Lanczos algorithm for computing (complex) linear response functions within the coupled cluster singles (CCS), coupled cluster singles and iterative approximate doubles (CC2), and coupled cluster singles and doubles (CCSD) is coupled to a Stieltjes imaging technique in order to describe the photoionization cross section of atoms and molecules, in the spirit of a similar procedure recently proposed by Averbukh and co-workers within the Algebraic Diagrammatic Construction approach. Pilot results are reported for the atoms He, Ne, and Ar and for the molecules H2, H2O, NH3, HF, CO, and CO2.

Influence of Aromatic Molecules on the Structure and Spectroscopy of Water Clusters

NASA Astrophysics Data System (ADS)

Tabor, Daniel P.; Sibert, Edwin; Walsh, Patrick S.; Zwier, Timothy S.

2016-06-01

Isomer-specific resonant ion-dip infrared spectra are presented for benzene-(water)_n, 1-2-diphenoxyethane-(water)_n, and tricyclophane-(water)_n clusters. The IR spectra are modeled with a local mode Hamiltonian that was originally formulated for the analysis of benzene-(water)_n clusters with up to seven waters. The model accounts for stretch-bend Fermi coupling, which can complicate the IR spectra in the 3150-3300 cm-1 region. When the water clusters interact with each of the solutes, the hydrogen bond lengths between the water molecules change in a characteristic way, reflecting the strength of the solute-water interaction. These structural effects are also reflected spectroscopically in the shifts of the local mode OH stretch frequencies. When diphenoxyethane is the solute, the water clusters distort more significantly than when bound to benzene. Tricyclophane's structure provides an aromatic-rich binding pocket for the water clusters. The local mode model is used to extract Hamiltonians for individual water molecules. These monomer Hamiltonians divide into groups based on their local H-bonding architecture, allowing for further classification of the wide variety of water environments encountered in this study.

Investigation of the local structure variance of water molecules in laser-induced thermal desorption process

NASA Astrophysics Data System (ADS)

Ju, Shin-Pon; Weng, Cheng-I.

2004-05-01

This paper presents the use of molecular dynamics simulation in the study of laser-induced thermal desorption (LITD) of water molecules adjacent to a laser-heated Au substrate. The local structure of the water molecules is investigated by considering the densities of the oxygen and hydrogen atoms, the average number of neighbors, nNN, and the average number of H-bonds, nHB. At an equilibrium temperature of 300 K, the simulation results show that three adsorption water layers are formed in the immediate vicinity of the Au surface, and that each four-fold hollow site on the uppermost Au(0 0 1) surface is occupied by a single water molecule. Following laser-induced heating of the Au substrate with a sub-picosecond laser pulse of 350 fs, the substrate temperature increases to 1000 K. This causes a gradual heating of the adjacent water film, which is accompanied by a decrease in the values of nNN and nHB. Hence, it can be concluded that an increase in the water film temperature destroys the hydrogen-bonding network throughout the water film. Although the maximum local temperature of the water film occurs in the region immediately adjacent to the Au substrate, it is determined that the attractive energy between the Au atoms and the water molecules in this region causes the water molecules to aggregate together to form three-dimensional water clusters. Furthermore, this energy prevents the hydrogen bonds in this region from breaking apart as violently as those within the phase explosion region. Finally, it is observed that the phase explosion phenomenon occurs in the region of the water film where the values of nNN and nHB are at a minimum.

Hydrated proton and hydroxide charge transfer at the liquid/vapor interface of water

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

Soniat, Marielle; Rick, Steven W., E-mail: srick@uno.edu; Kumar, Revati

2015-07-28

The role of the solvated excess proton and hydroxide ions in interfacial properties is an interesting scientific question with applications in a variety of aqueous behaviors. The role that charge transfer (CT) plays in interfacial behavior is also an unsettled question. Quantum calculations are carried out on clusters of water with an excess proton or a missing proton (hydroxide) to determine their CT. The quantum results are applied to analysis of multi-state empirical valence bond trajectories. The polyatomic nature of the solvated excess proton and hydroxide ion results in directionally dependent CT, depending on whether a water molecule is amore » hydrogen bond donor or acceptor in relation to the ion. With polyatomic molecules, CT also depends on the intramolecular bond distances in addition to intermolecular distances. The hydrated proton and hydroxide affect water’s liquid/vapor interface in a manner similar to monatomic ions, in that they induce a hydrogen-bonding imbalance at the surface, which results in charged surface waters. This hydrogen bond imbalance, and thus the charged waters at the surface, persists until the ion is at least 10 Å away from the interface.« less

Carbon Monoxide Hydrogenation on Ice Surfaces.

PubMed

Kuwahata, Kazuaki; Ohno, Kaoru

2018-03-14

We have performed density functional calculations to investigate the carbon monoxide hydrogenation reaction (H+CO→HCO), which is important in interstellar clouds. We found that the activation energy of the reaction on amorphous ice is lower than that on crystalline ice. In the course of this study, we demonstrated that it is roughly possible to use the excitation energy of the reactant molecule (CO) in place of the activation energy. This relationship holds also for small water clusters at the CCSD level of calculation and the two-layer-level ONIOM (CCSD : X3LYP) calculation. Generally, since it is computationally demanding to estimate activation energies of chemical reactions in a circumstance of many water molecules, this relationship enables one to determine the activation energy of this reaction on ice surfaces from the knowledge of the excitation energy of CO only. Incorporating quantum-tunneling effects, we discuss the reaction rate on ice surfaces. Our estimate that the reaction rate on amorphous ice is almost twice as large as that on crystalline ice is qualitatively consistent with the experimental evidence reported by Hidaka et al. [Chem. Phys. Lett., 2008, 456, 36.]. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Depth of focus extended microscope configuration for imaging of incorporated groups of molecules, DNA constructs and clusters inside bacterial cells

NASA Astrophysics Data System (ADS)

Fessl, Tomas; Ben-Yaish, Shai; Vacha, Frantisek; Adamec, Frantisek; Zalevsky, Zeev

2009-07-01

Imaging of small objects such as single molecules, DNA clusters and single bacterial cells is problematic not only due to the lateral resolution that is obtainable in currently existing microscopy but also, and as much fundamentally limiting, due to the lack of sufficient axial depth of focus to have the full object focused simultaneously. Extension in depth of focus is helpful also for single molecule steady state FRET measurements. In this technique it is crucial to obtain data from many well focused molecules, which are often located in different axial depths. In this paper we present the implementation of an all-optical and a real time technique of extension in the depth of focus that may be incorporated in any high NA microscope system and to be used for the above mentioned applications. We demonstrate experimentally how after the integration of special optical element in high NA 100× objective lens of a single molecule imaging microscope system, the depth of focus is significantly improved while maintaining the same lateral resolution in imaging applications of incorporated groups of molecules, DNA constructs and clusters inside bacterial cells.

Construction of Hyaluronic Tetrasaccharide Clusters Modified Polyamidoamine siRNA Delivery System.

PubMed

Ma, Yingcong; Sha, Meng; Cheng, Shixuan; Yao, Wang; Li, Zhongjun; Qi, Xian-Rong

2018-06-14

The CD44 protein, as a predominant receptor for hyaluronan (HA), is highly expressed on the surface of multiple tumor cells. HA, as a targeting molecule for a CD44-contained delivery system, increases intracellular drug concentration in tumor tissue. However, due to the weak binding ability of hyaluronan oligosaccharide to CD44, targeting for tumor drug delivery has been restricted. In this study, we first use a HA tetrasaccharide cluster as the target ligand to enhance the binding ability to CD44. A polyamidoamine (PAMAM) dendrimer was modified by a HA tetrasaccharide cluster as a nonviral vector for small interfering RNA (siRNA) delivery. The dendrimer/siRNA nanocomplexes increased the cellular uptake capacity of siRNA through the CD44 receptor-mediated endocytosis pathway, allowing the siRNA to successfully escape the endosome/lysosome. Compared with the control group, nanocomplexes effectively reduced the expression of GFP protein and mRNA in MDA-MB-231-GFP cells. This delivery system provides a foundation to increase the clinical applications of PAMAM nanomaterials.

Cluster formation in laser-induced ablation and evaporation of solids observed by laser ionization time-of-flight mass spectrometry and scanning tunneling microscopy

NASA Astrophysics Data System (ADS)

Tench, R. J.; Balooch, M.; Bernardez, L.; Allen, Mike J.; Siekhaus, W. J.; Olander, D. R.; Wang, W.

1990-04-01

Laser ionization time-of-flight mass analysis (LIMA) used pulses (5ns) of a frequency-quadrupled Nd-YAG laser (266 nm) focused onto spots of 4 to 100 microns diameter to ablate material, and a reflectron time of flight tube to mass-analyze the plume. The observed mass spectra for Si, Pt, SiC, and UO 2 varied in the distribution of ablation products among atoms, molecules and clusters, depending on laser power density and target material. Cleaved surfaces of highly oriented pyrolytic graphite (HOPG) positioned at room temperature either 10 cm away from materials ablated at 10(exp -5) Torr by 1 to 3 excimer laser (308 nm) pulses of 20 ns duration or 1 m away from materials vaporized at 10(exp -8) Torr by 10 Nd-Glass laser pulses of 1 ms duration were analyzed by Scanning Tunneling Microscopy (STM) in air with angstrom resolution. Clusters up to 30 A in diameter were observed.

C60 superstructure and carbide formation on the Al-terminated Al9Co2(001 ) surface

NASA Astrophysics Data System (ADS)

Ledieu, J.; Gaudry, É.; de Weerd, M.-C.; Gille, P.; Diehl, R. D.; Fournée, V.

2015-04-01

We report the formation of an ordered C60 monolayer on the Al9Co2 (001) surface using scanning tunneling microscopy (STM), low-energy electron diffraction (LEED), x-ray and ultraviolet photoelectron spectroscopy (XPS/UPS), and ab initio calculations. Dosing fullerenes at 300 K results in a disordered overlayer. However, the adsorption of C60 with the sample held between 573-673 K leads to a [4, -2 ∣1 ,3 ] phase. The growth of C60 proceeds with the formation of two domains which are mirror symmetric with respect to the [100] direction. Within each domain, the superstructure unit cell contains six molecules and this implies an area per fullerene equal to 91 Å2. The molecules exhibit two types of contrast (bright and dim) which are bias dependent. The adsorption energies and preferred molecular configuration at several possible adsorption sites have been determined theoretically. These calculations lead to a possible scheme describing the configuration of each C60 in the observed superstructure. Several defects (vacancies, protrusions,…) and domain boundaries observed in the film are also discussed. If the sample temperature is higher than 693 K when dosing, impinging C60 molecules dissociate at the surface, hence leading to the formation of a carbide film as observed by STM and LEED measurements. The formation of Al4C3 domains and the molecular dissociation are confirmed by XPS/UPS measurements acquired at different stages of the experiment. The cluster substructure present at the Al9Co2 (001) surface dictates the carbide domain orientations.

Constructing simple yet accurate potentials for describing the solvation of HCl/water clusters in bulk helium and nanodroplets.

PubMed

Boese, A Daniel; Forbert, Harald; Masia, Marco; Tekin, Adem; Marx, Dominik; Jansen, Georg

2011-08-28

The infrared spectroscopy of molecules, complexes, and molecular aggregates dissolved in superfluid helium clusters, commonly called HElium NanoDroplet Isolation (HENDI) spectroscopy, is an established, powerful experimental technique for extracting high resolution ro-vibrational spectra at ultra-low temperatures. Realistic quantum simulations of such systems, in particular in cases where the solute is undergoing a chemical reaction, require accurate solute-helium potentials which are also simple enough to be efficiently evaluated over the vast number of steps required in typical Monte Carlo or molecular dynamics sampling. This precludes using global potential energy surfaces as often parameterized for small complexes in the realm of high-resolution spectroscopic investigations that, in view of the computational effort imposed, are focused on the intermolecular interaction of rigid molecules with helium. Simple Lennard-Jones-like pair potentials, on the other hand, fall short in providing the required flexibility and accuracy in order to account for chemical reactions of the solute molecule. Here, a general scheme of constructing sufficiently accurate site-site potentials for use in typical quantum simulations is presented. This scheme employs atom-based grids, accounts for local and global minima, and is applied to the special case of a HCl(H(2)O)(4) cluster solvated by helium. As a first step, accurate interaction energies of a helium atom with a set of representative configurations sampled from a trajectory following the dissociation of the HCl(H(2)O)(4) cluster were computed using an efficient combination of density functional theory and symmetry-adapted perturbation theory, i.e. the DFT-SAPT approach. For each of the sampled cluster configurations, a helium atom was placed at several hundred positions distributed in space, leading to an overall number of about 400,000 such quantum chemical calculations. The resulting total interaction energies, decomposed into several energetic contributions, served to fit a site-site potential, where the sites are located at the atomic positions and, additionally, pseudo-sites are distributed along the lines joining pairs of atom sites within the molecular cluster. This approach ensures that this solute-helium potential is able to describe both undissociated molecular and dissociated (zwitter-) ionic configurations, as well as the interconnecting reaction pathway without re-adjusting partial charges or other parameters depending on the particular configuration. Test calculations of the larger HCl(H(2)O)(5) cluster interacting with helium demonstrate the transferability of the derived site-site potential. This specific potential can be readily used in quantum simulations of such HCl/water clusters in bulk helium or helium nanodroplets, whereas the underlying construction procedure can be generalized to other molecular solutes in other atomic solvents such as those encountered in rare gas matrix isolation spectroscopy.

N(2)O in small para-hydrogen clusters: Structures and energetics.

PubMed

Zhu, Hua; Xie, Daiqian

2009-04-30

We present the minimum-energy structures and energetics of clusters of the linear N(2)O molecule with small numbers of para-hydrogen molecules with pairwise additive potentials. Interaction energies of (p-H(2))-N(2)O and (p-H(2))-(p-H(2)) complexes were calculated by averaging the corresponding full-dimensional potentials over the H(2) angular coordinates. The averaged (p-H(2))-N(2)O potential has three minima corresponding to the T-shaped and the linear (p-H(2))-ONN and (p-H(2))-NNO structures. Optimization of the minimum-energy structures was performed using a Genetic Algorithm. It was found that p-H(2) molecules fill three solvation rings around the N(2)O axis, each of them containing up to five p-H(2) molecules, followed by accumulation of two p-H(2) molecules at the oxygen and nitrogen ends. The first solvation shell is completed at N = 17. The calculated chemical potential oscillates with cluster size up to the completed first solvation shell. These results are consistent with the available experimental measurements. (c) 2009 Wiley Periodicals, Inc.

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

Hormain, Laureline; Monnerville, Maurice, E-mail: maurice.monnerville@univ-lille1.fr; Toubin, Céline

The chlorine/water interface is of crucial importance in the context of atmospheric chemistry. Modeling the structure and dynamics at this interface requires an accurate description of the interaction potential energy surfaces. We propose here an analytical intermolecular potential that reproduces the interaction between the Cl{sub 2} molecule and a water molecule. Our functional form is fitted to a set of high level ab initio data using the coupled-cluster single double (triple)/aug-cc-p-VTZ level of electronic structure theory for the Cl{sub 2} − H{sub 2}O complex. The potential fitted to reproduce the three minima structures of 1:1 complex is validated by themore » comparison of ab initio results of Cl{sub 2} interacting with an increasing number of water molecules. Finally, the model potential is used to study the physisorption of Cl{sub 2} on a perfectly ordered hexagonal ice slab. The calculated adsorption energy, in the range 0.27 eV, shows a good agreement with previous experimental results.« less

The closo-Si{sub 12}C{sub 12} molecule from cluster to crystal: A theoretical prediction

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

Duan, Xiaofeng F., E-mail: xiaofeng.duan@wpafb.af.mil, E-mail: larry.burggraf@us.af.mil; Air Force Institute of Technology, Wright-Patterson Air Force Base, Ohio 45433; Burggraf, Larry W., E-mail: xiaofeng.duan@wpafb.af.mil, E-mail: larry.burggraf@us.af.mil

2016-03-21

The structure of closo-Si{sub 12}C{sub 12} is unique among stable Si{sub n}C{sub m} isomers (n, m > 4) because of its high symmetry, π–π stacking of C{sub 6} rings and unsaturated silicon atoms at symmetrical peripheral positions. Dimerization potential surfaces reveal various dimerization reactions that form between two closo-Si{sub 12}C{sub 12} molecules through Si–Si bonds at unsaturated Si atoms. As a result the closo-Si{sub 12}C{sub 12} molecule is capable of polymerization to form stable 1D polymer chains, 2D crystal layers, and 3D crystals. 2D crystal structures formed by side-side polymerization satisfy eight Si valences on each monomer without large distortionmore » of the monomer structure. 3D crystals are formed by stacking 2D structures in the Z direction, preserving registry of C{sub 6} rings in monomer moiety.« less

Dynamics of Lysozyme in a Glycerol-Water system

NASA Astrophysics Data System (ADS)

Ghatty, Pavan; Carri, Gustavo

2007-03-01

Bio-preservation of proteins is of great commercial and academic interest. A variety of sugars have been found to be effective in preserving the structure of proteins. This has been attributed and in some cases proved to their ability to form strong hydrogen bonds with proteins thus restricting their motion. The work presented here explores the hypothesis that glycerol, a tri-alcohol curbs the motion of protein. We have carried out a 10ns Molecular Dynamics simulation to study the phenomenon. The structure of Lysozyme (PDB code 193L) has been studied in three solutions of 10, 20 and 30 % by weight of glycerol in water. Glycerol molecules in all three solutions have shown a tendency to agglomerate around the protein. Strong hydrogen bonding has also been observed between glycerol molecules and the protein. With increasing time, the g(r) of glycerol molecules around proteins shows two peaks with increasing prominence suggesting the movement of glycerol cluster to positions closer to the protein surface.

The Reovirus Sigmal Aspartic Acid Sandwich: A Trimerization Motif Poised for Conformational Change

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

Schelling,P.; Guglielml, K.; Kirchner, E.

2007-01-01

Reovirus attachment protein {sigma}1 mediates engagement of receptors on the surface of target cells and undergoes dramatic conformational rearrangements during viral disassembly in the endocytic pathway. The {sigma}1 protein is a filamentous, trimeric molecule with a globular {beta}-barrel head domain. An unusual cluster of aspartic acid residues sandwiched between hydrophobic tyrosines is located at the {sigma}1 subunit interface. A 1.75 {angstrom} structure of the {sigma}1 head domain now reveals two water molecules at the subunit interface that are held strictly in position and interact with neighboring residues. Structural and biochemical analyses of mutants affecting the aspartic acid sandwich indicate thatmore » these residues and the corresponding chelated water molecules act as a plug to block the free flow of solvent and stabilize the trimer. This arrangement of residues at the {sigma}1 head trimer interface illustrates a new protein design motif that may confer conformational mobility during cell entry.« less

Insulin promotes cell migration by regulating PSA-NCAM.

PubMed

Monzo, Hector J; Coppieters, Natacha; Park, Thomas I H; Dieriks, Birger V; Faull, Richard L M; Dragunow, Mike; Curtis, Maurice A

2017-06-01

Cellular interactions with the extracellular environment are modulated by cell surface polysialic acid (PSA) carried by the neural cell adhesion molecule (NCAM). PSA-NCAM is involved in cellular processes such as differentiation, plasticity, and migration, and is elevated in Alzheimer's disease as well as in metastatic tumour cells. Our previous work demonstrated that insulin enhances the abundance of cell surface PSA by inhibiting PSA-NCAM endocytosis. In the present study we have identified a mechanism for insulin-dependent inhibition of PSA-NCAM turnover affecting cell migration. Insulin enhanced the phosphorylation of the focal adhesion kinase leading to dissociation of αv-integrin/PSA-NCAM clusters, and promoted cell migration. Our results show that αv-integrin plays a key role in the PSA-NCAM turnover process. αv-integrin knockdown stopped PSA-NCAM from being endocytosed, and αv-integrin/PSA-NCAM clusters co-labelled intracellularly with Rab5, altogether indicating a role for αv-integrin as a carrier for PSA-NCAM during internalisation. Furthermore, inhibition of p-FAK caused dissociation of αv-integrin/PSA-NCAM clusters and counteracted the insulin-induced accumulation of PSA at the cell surface and cell migration was impaired. Our data reveal a functional association between the insulin/p-FAK-dependent regulation of PSA-NCAM turnover and cell migration through the extracellular matrix. Most importantly, they identify a novel mechanism for insulin-stimulated cell migration. Copyright © 2017 Elsevier Inc. All rights reserved.

Sensing based on surface-enhanced Raman scattering using self-forming ZnO nanoarrays coated with gold as substrates

NASA Astrophysics Data System (ADS)

Tang, Feng; Adam, Pierre-Michel; Rogers, David J.; Sandana, Vinod E.; Bove, Philippe; Teherani, Ferechteh H.

2018-03-01

Surface-Enhanced Raman spectroscopy (SERS) is a widely used technique adopted in both academia and industry for the detection of trace quantities of Raman active molecules. This is usually accomplished by functionalizing distributions of plasmonic metal nanoparticles with the analyte molecules. Recently metal-coated nanostructures have been investigated as alternatives to dispersions of metal nanoparticles in order to avoid clustering and homogeneity/reproducibility issues. In this paper, several samples of Au-coated ZnO nanoarrays are adopted as SERS substrates in order to investigate the molecular sensing capacity for methylene blue (MB) molecules. Self-forming ZnO nanoarrays were grown on both c-sapphire and silicon substrates by pulsed laser deposition. The nanoarrays were then coated with 30 nm of gold using thermal evaporation and the SERS signals of MB functionalized samples were obtained with a Raman microspectrometer. The ratio of SERS intensity to that of an MB functionalized glass substrate (ISERS/IRaman) was calculated based on the averaged SERS signals. A relatively good within-wafer homogeneity of the enhancement effect was found with ISERS/IRaman values as high as 64.2 for Au-coated nano ZnO grown on silicon substrates. The experimental results show that the Au-coated ZnO nanoarrays can be excellent SERS substrates for molecular/chemical analyte sensing.

Theoretical study of the interaction of N/sub 2/ with water molecules. (H/sub 2/O)/sub n/:N/sub 2/, n = 1--8

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

Curtiss, L.A.; Eisgruber, C.L.

1984-03-01

Ab initio molecular orbital calculations including correlation energy have been carried out on the interaction of a single H/sub 2/O molecule with N/sub 2/. The potential energy surface for H/sub 2/O:N/sub 2/ is found to have a minimum corresponding to a HOH xxx N/sub 2/ structure with a weak (<2 kcal mol/sup -1/) hydrogen bond. A second, less stable, configuration corresponding to a H/sub 2/O xxx N/sub 2/ structure with N/sub 2/ bonded side on to the oxygen of H/sub 2/O was found to be either a minimum or a saddle point in the potential energy surface depending on themore » level of calculation. The minimal STO-3G basis set was used to investigate the interaction of up to eight H/sub 2/O molecules with N/sub 2/. Two types of clusters, one containing only HOH xxx N/sub 2/ interactions and the other containing both HOH xxxN/sub 2/ and H/sub 2/O xxx N/sub 2/ interactions, were investigated for (N/sub 2/:(H/sub 2/O)/sub n/, n = 2--8).« less

The Neural Cell Adhesion Molecule (NCAM) Promotes Clustering and Activation of EphA3 Receptors in GABAergic Interneurons to Induce Ras Homolog Gene Family, Member A (RhoA)/Rho-associated protein kinase (ROCK)-mediated Growth Cone Collapse*

PubMed Central

Sullivan, Chelsea S.; Kümper, Maike; Temple, Brenda S.; Maness, Patricia F.

2016-01-01

Establishment of a proper balance of excitatory and inhibitory connectivity is achieved during development of cortical networks and adjusted through synaptic plasticity. The neural cell adhesion molecule (NCAM) and the receptor tyrosine kinase EphA3 regulate the perisomatic synapse density of inhibitory GABAergic interneurons in the mouse frontal cortex through ephrin-A5-induced growth cone collapse. In this study, it was demonstrated that binding of NCAM and EphA3 occurred between the NCAM Ig2 domain and EphA3 cysteine-rich domain (CRD). The binding interface was further refined through molecular modeling and mutagenesis and shown to be comprised of complementary charged residues in the NCAM Ig2 domain (Arg-156 and Lys-162) and the EphA3 CRD (Glu-248 and Glu-264). Ephrin-A5 induced co-clustering of surface-bound NCAM and EphA3 in GABAergic cortical interneurons in culture. Receptor clustering was impaired by a charge reversal mutation that disrupted NCAM/EphA3 association, emphasizing the importance of the NCAM/EphA3 binding interface for cluster formation. NCAM enhanced ephrin-A5-induced EphA3 autophosphorylation and activation of RhoA GTPase, indicating a role for NCAM in activating EphA3 signaling through clustering. NCAM-mediated clustering of EphA3 was essential for ephrin-A5-induced growth cone collapse in cortical GABAergic interneurons, and RhoA and a principal effector, Rho-associated protein kinase, mediated the collapse response. This study delineates a mechanism in which NCAM promotes ephrin-A5-dependent clustering of EphA3 through interaction of the NCAM Ig2 domain and the EphA3 CRD, stimulating EphA3 autophosphorylation and RhoA signaling necessary for growth cone repulsion in GABAergic interneurons in vitro, which may extend to remodeling of axonal terminals of interneurons in vivo. PMID:27803162

Optical and Atomic Force Microscopy Characterization of PbI2 Quantum Dots

NASA Technical Reports Server (NTRS)

Mu, R.; Tung, Y. S.; Ueda, A.; Henderson, D. O.

1997-01-01

Lead iodide (PbI2) clusters were synthesized from the chemical reaction of NaI (or KI) with Pb(NO3)2 in H2O, D2O, CH3OH, and C3H7OH media. The observation of the absorption features above 350 nm with the help of integrating sphere accessory strongly suggests the quantum dot formation of PbI2 in solution. Spectral comparison between the synthesized PbI2 clusters in solution and PbI2 nanophase by impregnation of PbI2 in four different pore-sized porous silica indicates that the PbI2 cluster size in solution is less than 2.5 nm in lateral dimension. Atomic force microscopy (AFM) measurements show that the PbL clusters deposited onto three different molecularly flat surfaces are single-layered. The measured height is 1.0 - 0.1 nm. The swollen layer thickness can be attributed to the intralayer contraction from the strong lateral interaction among PbI2 molecules, which is supported by ab initio calculation. Raman scattering measurement of LO and TO modes of PbI2 in bulk and in the confined state were also conducted in 50-150 cu cm region. The observed three bands at 74, %, 106 1/cm are assigned to TO2, LO2, and LO, mode, respectively. The relatively small red-shift in LO modes may be caused by the surface phonon polaritons of PbI2 nanophase in the porous silica.

L-Tryptophan on Cu(111): engineering a molecular labyrinth driven by indole groups

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

Yitamben, E. N.; Clayborne, A.; Darling, Seth B.

2015-05-21

The present article investigates the adsorption and molecular orientation of L-Tryptophan, which is both an essential amino acid important for protein synthesis and of particular interest for the development of chiral molecular electronics and biocompatible processes and devices, on Cu(111) using scanning tunneling microscopy and spectroscopy at 55 K and at room temperature. The arrangement of chemisorbed L-Tryptophan on the copper surface varies with both temperature and surface coverage. At low coverage, small clusters form on the surface irrespective of temperature, while at high coverage an ordered chain structure emerges at room temperature, and a tightly packed structure forms amore » molecular labyrinth at low temperature. The dominating superstructure of the adsorbates arises from intermolecular hydrogen bonding, and pi-bonding interactions between the indole groups of neighboring molecules and the Cu surface.« less

A Hybrid Density Functional Theory/Molecular Mechanics Approach for Linear Response Properties in Heterogeneous Environments.

PubMed

Rinkevicius, Zilvinas; Li, Xin; Sandberg, Jaime A R; Mikkelsen, Kurt V; Ågren, Hans

2014-03-11

We introduce a density functional theory/molecular mechanical approach for computation of linear response properties of molecules in heterogeneous environments, such as metal surfaces or nanoparticles embedded in solvents. The heterogeneous embedding environment, consisting from metallic and nonmetallic parts, is described by combined force fields, where conventional force fields are used for the nonmetallic part and capacitance-polarization-based force fields are used for the metallic part. The presented approach enables studies of properties and spectra of systems embedded in or placed at arbitrary shaped metallic surfaces, clusters, or nanoparticles. The capability and performance of the proposed approach is illustrated by sample calculations of optical absorption spectra of thymidine absorbed on gold surfaces in an aqueous environment, where we study how different organizations of the gold surface and how the combined, nonadditive effect of the two environments is reflected in the optical absorption spectrum.

Theoretical study on microhydration of SeO42-: On the number of water molecules necessary to stabilize the dianion

NASA Astrophysics Data System (ADS)

Pathak, Arup Kumar

2012-01-01

Microhydration of SeO42-·nH2O (n = 1-5) clusters are reported at B3LYP/Aug-cc-pvtz level of theory. Lower size hydrated clusters are stabilized by only double-hydrogen-bonding arrangements and the most stable conformer for higher size cluster (n > 3) contains a cyclic water ring. It is observed that at least one water molecule is necessary to stabilize the dianion in the gas phase against spontaneous electron loss. The microscopic theory based expression provides a route to predict the instability of bare SeO42- and to obtain the VDE for a wide range of cluster sizes including the bulk from the knowledge of the same for a few stable hydrated clusters.

Ab initio simulations of scanning-tunneling-microscope images with embedding techniques and application to C58-dimers on Au(111).

PubMed

Wilhelm, Jan; Walz, Michael; Stendel, Melanie; Bagrets, Alexei; Evers, Ferdinand

2013-05-14

We present a modification of the standard electron transport methodology based on the (non-equilibrium) Green's function formalism to efficiently simulate STM-images. The novel feature of this method is that it employs an effective embedding technique that allows us to extrapolate properties of metal substrates with adsorbed molecules from quantum-chemical cluster calculations. To illustrate the potential of this approach, we present an application to STM-images of C58-dimers immobilized on Au(111)-surfaces that is motivated by recent experiments.

Potential energy surfaces of the ground and low-lying states of HCCS and NCS: CASSCF, MRCI and CCSD(T) studies

NASA Astrophysics Data System (ADS)

Li, Yumin; Iwata, Suehiro

1997-07-01

For astronomically interesting molecules, HCCS and NCS, the equilibrium geometries and potential energy curves of three states (X 2Π, A 2Π and B 2Σ+) as well as vertical excitation energies are studied using complete active space SCF (CASSCF), multi-reference configuration interaction (MRCI) and coupled cluster (CCSD(T)) methods with cc-pVTZ basis sets. The difference and similarity in the three states of HCCS and NCS are illustrated. The results obtained are in good agreement with available experimental data.

The role of electronegativity on the extent of nitridation of group 5 metals as revealed by reactions of tantalum cluster cations with ammonia molecules.

PubMed

Arakawa, Masashi; Ando, Kota; Fujimoto, Shuhei; Mishra, Saurabh; Patwari, G Naresh; Terasaki, Akira

2018-05-10

Reactions of the free tantalum cation, Ta+, and tantalum cluster cations, Tan+ (n = 2-10), with ammonia are presented. The reaction of the monomer cation, Ta+, with two molecules of NH3 leads to the formation of TaN2H2+ along with release of two H2 molecules. The dehydrogenation occurs until the formal oxidation number of the tantalum atom reaches +5. On the other hand, all the tantalum cluster cations, Tan+, react with two molecules of NH3 and form TanN2+ with the release of three H2 molecules. Further exposure to ammonia showed that TanNmH+ and TanNm+ are produced through successive reactions; a pure nitride and three H2 molecules are formed for every other NH3 molecule. The nitridation occurred until the formal oxidation number of the tantalum atoms reaches +5 as in the case of TaN2H2+ in contrast to other group 5 elements, i.e., vanadium and niobium, which have been reported to produce nitrides with lower oxidation states. The present results on small gas-phase metal-nitride clusters show correlation with their bulk properties: tantalum is known to form bulk nitrides in the oxidation states of either +5 (Ta3N5) or +3 (TaN), whereas vanadium and niobium form nitrides in the oxidation state of +3 (VN and NbN). Along with DFT calculations, these findings reveal that nitridation is driven by the electron-donating ability of group 5 elements, i.e., electronegativity of the metal plays a key role in determining the composition of the metal nitrides.

Defining scaffold geometries for interacting with proteins: geometrical classification of secondary structure linking regions.

PubMed

Tran, Tran T; Kulis, Christina; Long, Steven M; Bryant, Darryn; Adams, Peter; Smythe, Mark L

2010-11-01

Medicinal chemists synthesize arrays of molecules by attaching functional groups to scaffolds. There is evidence suggesting that some scaffolds yield biologically active molecules more than others, these are termed privileged substructures. One role of the scaffold is to present its side-chains for molecular recognition, and biologically relevant scaffolds may present side-chains in biologically relevant geometries or shapes. Since drug discovery is primarily focused on the discovery of compounds that bind to proteinaceous targets, we have been deciphering the scaffold shapes that are used for binding proteins as they reflect biologically relevant shapes. To decipher the scaffold architecture that is important for binding protein surfaces, we have analyzed the scaffold architecture of protein loops, which are defined in this context as continuous four residue segments of a protein chain that are not part of an α-helix or β-strand secondary structure. Loops are an important molecular recognition motif of proteins. We have found that 39 clusters reflect the scaffold architecture of 89% of the 23,331 loops in the dataset, with average intra-cluster and inter-cluster RMSD of 0.47 and 1.91, respectively. These protein loop scaffolds all have distinct shapes. We have used these 39 clusters that reflect the scaffold architecture of protein loops as biological descriptors. This involved generation of a small dataset of scaffold-based peptidomimetics. We found that peptidomimetic scaffolds with reported biological activities matched loop scaffold geometries and those peptidomimetic scaffolds with no reported biologically activities did not. This preliminary evidence suggests that organic scaffolds with tight matches to the preferred loop scaffolds of proteins, implies the likelihood of the scaffold to be biologically relevant.

Defining scaffold geometries for interacting with proteins: geometrical classification of secondary structure linking regions

NASA Astrophysics Data System (ADS)

Tran, Tran T.; Kulis, Christina; Long, Steven M.; Bryant, Darryn; Adams, Peter; Smythe, Mark L.

2010-11-01

Medicinal chemists synthesize arrays of molecules by attaching functional groups to scaffolds. There is evidence suggesting that some scaffolds yield biologically active molecules more than others, these are termed privileged substructures. One role of the scaffold is to present its side-chains for molecular recognition, and biologically relevant scaffolds may present side-chains in biologically relevant geometries or shapes. Since drug discovery is primarily focused on the discovery of compounds that bind to proteinaceous targets, we have been deciphering the scaffold shapes that are used for binding proteins as they reflect biologically relevant shapes. To decipher the scaffold architecture that is important for binding protein surfaces, we have analyzed the scaffold architecture of protein loops, which are defined in this context as continuous four residue segments of a protein chain that are not part of an α-helix or β-strand secondary structure. Loops are an important molecular recognition motif of proteins. We have found that 39 clusters reflect the scaffold architecture of 89% of the 23,331 loops in the dataset, with average intra-cluster and inter-cluster RMSD of 0.47 and 1.91, respectively. These protein loop scaffolds all have distinct shapes. We have used these 39 clusters that reflect the scaffold architecture of protein loops as biological descriptors. This involved generation of a small dataset of scaffold-based peptidomimetics. We found that peptidomimetic scaffolds with reported biological activities matched loop scaffold geometries and those peptidomimetic scaffolds with no reported biologically activities did not. This preliminary evidence suggests that organic scaffolds with tight matches to the preferred loop scaffolds of proteins, implies the likelihood of the scaffold to be biologically relevant.

Stepwise hydration and evaporation of adenosine monophosphate nucleotide anions: a multiscale theoretical study.

PubMed

Calvo, F; Douady, J

2010-04-14

The structure and finite-temperature properties of hydrated nucleotide anion adenosine 5'-monophosphate (AMP) have been theoretically investigated with a variety of methods. Using a polarizable version of the Amber force field and replica-exchange molecular dynamics simulations, putative lowest-energy structures have been located for the AMP(-)(H(2)O)(n) cluster anions with n = 0-20. The hydration energies obtained with the molecular mechanics potential slightly overestimate experimental measurements. However, closer values are found after reoptimizing the structures locally at more sophisticated levels, namely semi-empirical (PM6) and density-functional theory (B3LYP/6-31+G*). Upon heating the complexes, various indicators such as the heat capacity, number of hydrogen bonds or surface area provide evidence that the water cluster melts below 200 K but remains bonded to the AMP anion. The sequential loss of water molecules after sudden heating has been studied using a statistical approach in which unimolecular evaporation is described using the orbiting transition state version of phase space theory, together with anharmonic densities of vibrational states. The evaporation rates are calibrated based on the results of molecular dynamics trajectories at high internal energy. Our results indicate that between 4 and 10 water molecules are lost from AMP(-)(H(2)O)(20) after one second depending on the initial heating in the 250-350 K range, with a concomitant cooling of the remaining cluster by 75-150 K.

Infrared Spectroscopy of Metal Ion Complexes: Models for Metal Ligand Interactions and Solvation

NASA Astrophysics Data System (ADS)

Duncan, Michael

2006-03-01

Weakly bound complexes of the form M^+-Lx (M=Fe, Ni, Co, etc.; L=CO2, C2H2, H2O, benzene, N2) are prepared in supersonic molecular beams by laser vaporization in a pulsed-nozzle cluster source. These species are mass analyzed and size-selected in a reflectron time-of-flight mass spectrometer. Clusters are photodissociated at infrared wavelengths with a Nd:YAG pumped infrared optical parametric oscillator/amplifier (OPO/OPA) laser or with a tunable infrared free-electron laser. M^+-(CO2)x complexes absorb near the free CO2 asymmetric stretch near 2349 cm-1 but with an interesting size dependent variation in the resonances. Small clusters have blue-shifted resonances, while larger complexes have additional bands due to surface CO2 molecules not attached to the metal. M^+(C2H2)n complexes absorb near the C-H stretches in acetylene, but resonances in metal complexes are red-shifted with repect to the isolated molecule. Ni^+ and Co^+ complexes with acetylene undergo intracluster cyclization reactions to form cyclobutadiene. Transition metal water complexes are studied in the O-H stretch region, and partial rotational structure can be measured. M^+(benzene) and M^+(benzene)2 ions (M=V, Ti, Al) represent half-sandwich and sandwich species, whose spectra are measured near the free benzene modes. These new IR spectra and their assignments will be discussed as well as other new IR spectra for similar complexes.

Paramagnetic Attraction of Impurity-Helium Solids

NASA Technical Reports Server (NTRS)

Bernard, E. P.; Boltnev, R. E.; Khmelenko, V. V.; Lee, D. M.

2003-01-01

Impurity-helium solids are formed when a mixture of impurity and helium gases enters a volume of superfluid helium. Typical choices of impurity gas are hydrogen deuteride, deuterium, nitrogen, neon and argon, or a mixture of these. These solids consist of individual impurity atoms and molecules as well as clusters of impurity atoms and molecules covered with layers of solidified helium. The clusters have an imperfect crystalline structure and diameters ranging up to 90 angstroms, depending somewhat on the choice of impurity. Immediately following formation the clusters aggregate into loosely connected porous solids that are submerged in and completely permeated by the liquid helium. Im-He solids are extremely effective at stabilizing high concentrations of free radicals, which can be introduced by applying a high power RF dis- charge to the impurity gas mixture just before it strikes the super fluid helium. Average concentrations of 10(exp 19) nitrogen atoms/cc and 5 x 10(exp 18) deuterium atoms/cc can be achieved this way. It shows a typical sample formed from a mixture of atomic and molecular hydrogen and deuterium. It shows typical sample formed from atomic and molecular nitrogen. Much of the stability of Im-He solids is attributed to their very large surface area to volume ratio and their permeation by super fluid helium. Heat resulting from a chance meeting and recombination of free radicals is quickly dissipated by the super fluid helium instead of thermally promoting the diffusion of other nearby free radicals.

On the existence of Rydberg nuclear molecules

NASA Astrophysics Data System (ADS)

Bertulani, C. A.; Frederico, T.; Hussein, M. S.

2017-11-01

Present nuclear detection techniques prevents us from determining if the analogue of a Rydberg molecule exists for the nuclear case. But nothing in nature disallows their existence. As in the atomic case, Rydberg nuclear molecules would be a laboratory for new aspects and applications of nuclear physics. We propose that Rydberg nuclear molecules, which represent the exotic, halo nuclei version, such as 11Be +11Be, of the well known quasimolecules observed in stable nuclei such as 12C +12C, might be common structures that could manifest their existence along the dripline. A study of possible candidates and the expected structure of such exotic clustering of two halo nuclei: the Rydberg nuclear molecules, is made on the basis of three different methods. It is shown that such cluster structures might be stable and unexpectedly common.

Electron correlation in real time.

PubMed

Sansone, Giuseppe; Pfeifer, Thomas; Simeonidis, Konstantinos; Kuleff, Alexander I

2012-02-01

Electron correlation, caused by the interaction among electrons in a multielectron system, manifests itself in all states of matter. A complete theoretical description of interacting electrons is challenging; different approximations have been developed to describe the fundamental aspects of the correlation that drives the evolution of simple (few-electron systems in atoms/molecules) as well as complex (multielectron wave functions in atoms, molecules, and solids) systems. Electron correlation plays a key role in the relaxation mechanisms that characterize excited states of neutral or ionized atoms and molecules populated by absorption of extreme ultraviolet (XUV) or X-ray radiation. The dynamics of these states can lead to different processes such as Fano resonance and Auger decay in atoms or interatomic Coulombic decay or charge migration in molecules and clusters. Many of these relaxation mechanisms are ubiquitous in nature and characterize the interaction of complex systems, such as biomolecules, adsorbates on surfaces, and hydrogen-bonded clusters, with XUV light. These mechanisms evolve typically on the femtosecond (1 fs=10(-15) s) or sub-femtosecond timescale. The experimental availability of few-femtosecond and attosecond (1 as=10(-18) s) XUV pulses achieved in the last 10 years offers, for the first time, the opportunity to excite and probe in time these dynamics giving the possibility to trace and control multielectron processes. The generation of ultrashort XUV radiation has triggered the development and application of spectroscopy techniques that can achieve time resolution well into the attosecond domain, thereby offering information on the correlated electronic motion and on the correlation between electron and nuclear motion. A deeper understanding of how electron correlation works could have a large impact in several research fields, such as biochemistry and biology, and trigger important developments in the design and optimization of electronic devices. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Theoretical study of negatively charged Fe(-)-(H2O)(n ≤ 6) clusters.

PubMed

Castro, Miguel

2012-06-14

Interactions of a singly negatively charged iron atom with water molecules, Fe(-)-(H(2)O)(n≤6), in the gas phase were studied by means of density functional theory. All-electron calculations were performed using the B3LYP functional and the 6-311++G(2d,2p) basis set for the Fe, O, and H atoms. In the lowest total energy states of Fe(-)-(H(2)O)(n), the metal-hydrogen bonding is stronger than the metal-oxygen one, producing low-symmetry structures because the water molecules are directly attached to the metal by basically one of their hydrogen atoms, whereas the other ones are involved in a network of hydrogen bonds, which together with the Fe(δ-)-H(δ+) bonding accounts for the nascent hydration of the Fe(-) anion. For Fe(-)-(H(2)O)(3≤n), three-, four-, five-, and six-membered rings of water molecules are bonded to the metal, which is located at the surface of the cluster in such a way as to reduce the repulsion with the oxygen atoms. Nevertheless, internal isomers appear also, lying less than 3 or 5 kcal/mol for n = 2-3 or n = 4-6. These results are in contrast with those of classical TM(+)-(H(2)O)(n) complexes, where the direct TM(+)-O bonding usually produces high symmetry structures with the metal defining the center of the complex. They show also that the Fe(-) anions, as the TM(+) ions, have great capability for the adsorption of water molecules, forming Fe(-)-(H(2)O)(n) structures stabilized by Fe(δ-)-H(δ+) and H-bond interactions.

ReaxFF molecular dynamics simulation of intermolecular structure formation in acetic acid-water mixtures at elevated temperatures and pressures

NASA Astrophysics Data System (ADS)

Sengul, Mert Y.; Randall, Clive A.; van Duin, Adri C. T.

2018-04-01

The intermolecular structure formation in liquid and supercritical acetic acid-water mixtures was investigated using ReaxFF-based molecular dynamics simulations. The microscopic structures of acetic acid-water mixtures with different acetic acid mole fractions (1.0 ≥ xHAc ≥ 0.2) at ambient and critical conditions were examined. The potential energy surface associated with the dissociation of acetic acid molecules was calculated using a metadynamics procedure to optimize the dissociation energy of ReaxFF potential. At ambient conditions, depending on the acetic acid concentration, either acetic acid clusters or water clusters are dominant in the liquid mixture. When acetic acid is dominant (0.4 ≤ xHAc), cyclic dimers and chain structures between acetic acid molecules are present in the mixture. Both structures disappear at increased water content of the mixture. It was found by simulations that the acetic acid molecules released from these dimer and chain structures tend to stay in a dipole-dipole interaction. These structural changes are in agreement with the experimental results. When switched to critical conditions, the long-range interactions (e.g., second or fourth neighbor) disappear and the water-water and acetic acid-acetic acid structural formations become disordered. The simulated radial distribution function for water-water interactions is in agreement with experimental and computational studies. The first neighbor interactions between acetic acid and water molecules are preserved at relatively lower temperatures of the critical region. As higher temperatures are reached in the critical region, these interactions were observed to weaken. These simulations indicate that ReaxFF molecular dynamics simulations are an appropriate tool for studying supercritical water/organic acid mixtures.

Investigating the ground-state rotamers of n-propylperoxy radical.

PubMed

Hoobler, Preston R; Turney, Justin M; Schaefer, Henry F

2016-11-07

The n-propylperoxy radical has been described as a molecule of critical importance to studies of low temperature combustion. Ab initio methods were used to study this three-carbon alkylperoxy radical, normal propylperoxy. Reliable CCSD(T) (coupled-cluster theory, incorporating single, double, and perturbative triple)/ANO0 geometries were predicted for the molecule's five rotamers. For each rotamer, energetic predictions were made using basis sets as large as the cc-pV5Z in conjunction with coupled cluster levels of theory up to CCSDT(Q). Along with the extrapolations, corrections for relativistic effects, zero-point vibrational energies, and diagonal Born-Oppenheimer corrections were used to further refine energies. The results indicate that the lowest conformer is the gauche-gauche (GG) rotamer followed by the gauche-trans (0.12 kcal mol -1 above GG), trans-gauche (0.44 kcal mol -1 ), gauche'-gauche (0.47 kcal mol -1 ), and trans-trans (0.57 kcal mol -1 ). Fundamental vibrational frequencies were obtained using second-order vibrational perturbation theory. This is the first time anharmonic frequencies have been computed for this system. The most intense IR features include all but one of the C-H stretches. The O-O fundamental (1063 cm -1 for the GG structure) also has a significant IR intensity, 19.6 km mol -1 . The anharmonicity effects on the potential energy surface were also used to compute vibrationally averaged r g,0K bond lengths, accounting for zero-point vibrations present within the molecule.

Investigating the ground-state rotamers of n-propylperoxy radical

NASA Astrophysics Data System (ADS)

Hoobler, Preston R.; Turney, Justin M.; Schaefer, Henry F.

2016-11-01

The n-propylperoxy radical has been described as a molecule of critical importance to studies of low temperature combustion. Ab initio methods were used to study this three-carbon alkylperoxy radical, normal propylperoxy. Reliable CCSD(T) (coupled-cluster theory, incorporating single, double, and perturbative triple)/ANO0 geometries were predicted for the molecule's five rotamers. For each rotamer, energetic predictions were made using basis sets as large as the cc-pV5Z in conjunction with coupled cluster levels of theory up to CCSDT(Q). Along with the extrapolations, corrections for relativistic effects, zero-point vibrational energies, and diagonal Born-Oppenheimer corrections were used to further refine energies. The results indicate that the lowest conformer is the gauche-gauche (GG) rotamer followed by the gauche-trans (0.12 kcal mol-1 above GG), trans-gauche (0.44 kcal mol-1), gauche'-gauche (0.47 kcal mol-1), and trans-trans (0.57 kcal mol-1). Fundamental vibrational frequencies were obtained using second-order vibrational perturbation theory. This is the first time anharmonic frequencies have been computed for this system. The most intense IR features include all but one of the C-H stretches. The O-O fundamental (1063 cm-1 for the GG structure) also has a significant IR intensity, 19.6 km mol-1. The anharmonicity effects on the potential energy surface were also used to compute vibrationally averaged rg,0K bond lengths, accounting for zero-point vibrations present within the molecule.

State-selective optimization of local excited electronic states in extended systems

NASA Astrophysics Data System (ADS)

Kovyrshin, Arseny; Neugebauer, Johannes

2010-11-01

Standard implementations of time-dependent density-functional theory (TDDFT) for the calculation of excitation energies give access to a number of the lowest-lying electronic excitations of a molecule under study. For extended systems, this can become cumbersome if a particular excited state is sought-after because many electronic transitions may be present. This often means that even for systems of moderate size, a multitude of excited states needs to be calculated to cover a certain energy range. Here, we present an algorithm for the selective determination of predefined excited electronic states in an extended system. A guess transition density in terms of orbital transitions has to be provided for the excitation that shall be optimized. The approach employs root-homing techniques together with iterative subspace diagonalization methods to optimize the electronic transition. We illustrate the advantages of this method for solvated molecules, core-excitations of metal complexes, and adsorbates at cluster surfaces. In particular, we study the local π →π∗ excitation of a pyridine molecule adsorbed at a silver cluster. It is shown that the method works very efficiently even for high-lying excited states. We demonstrate that the assumption of a single, well-defined local excitation is, in general, not justified for extended systems, which can lead to root-switching during optimization. In those cases, the method can give important information about the spectral distribution of the orbital transition employed as a guess.

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

PubMed

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.

Microsolvation of the potassium ion with aromatic rings: comparison between hexafluorobenzene and benzene.

PubMed

Marques, J M C; Llanio-Trujillo, J L; Albertí, M; Aguilar, A; Pirani, F

2013-08-22

We employ a recently developed methodology to study structural and energetic properties of the first solvation shells of the potassium ion in nonpolar environments due to aromatic rings, which is important to understand the selectivity of several biochemical phenomena. Our evolutionary algorithm is used in the global optimization study of clusters formed of K(+) solvated with hexafluorobenzene (HFBz) molecules. The global intermolecular interaction for these clusters has been decomposed in HFBz-HFBz and in K(+)-HFBz contributions, using a potential model based on different decompositions of the molecular polarizability of hexafluorobenzene. Putative global minimum structures of microsolvation clusters up to 21 hexafluorobenzene molecules were obtained and compared with the analogous K(+)-benzene clusters reported in our previous work (J. Phys. Chem. A 2012, 116, 4947-4956). We have found that both K(+)-(Bz)n and K(+)-(HFBz)n clusters show a strong magic number around the closure of the first solvation shell. Nonetheless, all K(+)-benzene clusters have essentially the same first solvation shell geometry with four solvent molecules around the ion, whereas the corresponding one for K(+)-(HFBz)n is completed with nine HFBz species, and its structural motif varies as n increases. This is attributed to the ion-solvent interaction that has a larger magnitude for K(+)-Bz than in the case of K(+)-HFBz. In addition, the ability of having more HFBz than Bz molecules around K(+) in the first solvation shell is intimately related to the inversion in the sign of the quadrupole moment of the two solvent species, which leads to a distinct ion-solvent geometry of approach.

Soft- and reactive landing of ions onto surfaces: Concepts and applications: CONCEPTS AND APPLICATIONS

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

Johnson, Grant E.; Gunaratne, Don; Laskin, Julia

2015-04-16

Soft- and reactive landing of mass-selected ions is gaining attention as a promising approach for the precisely-controlled preparation of materials on surfaces that are not amenable to deposition using conventional methods. A broad range of ionization sources and mass-filters are available that make ion soft-landing a versatile tool for surface modification using beams of hyperthermal (< 100 eV) ions. The ability to select the mass-to-charge ratio of the ion, its kinetic energy and charge state, along with precise control of the size, shape, and position of the ion beam on the deposition target distinguishes ion soft landing from other surfacemore » modification techniques. Soft- and reactive landing have been used to prepare interfaces for practical applications as well as precisely-defined model surfaces for fundamental investigations in chemistry, physics, and materials science. For instance, soft- and reactive landing have been applied to study the surface chemistry of ions isolated in the gas-phase, prepare arrays of proteins for high-throughput biological screening, produce novel carbon-based and polymer materials, enrich the secondary structure of peptides and the chirality of organic molecules, immobilize electrochemically-active proteins and organometallics on electrodes, create thin films of complex molecules, and immobilize catalytically active organometallics as well as ligated metal clusters. In addition, soft landing has enabled investigation of the size-dependent behavior of bare metal clusters in the critical subnanometer size regime where chemical and physical properties do not scale predictably with size. The morphology, aggregation, and immobilization of larger bare metal nanoparticles, which are directly relevant to the design of catalysts as well as improved memory and electronic devices, have also been studied using ion soft landing. This review article begins in section 1 with a brief introduction to the existing applications of ion soft- and reactive landing. Section 2 provides an overview of the ionization sources and mass filters that have been used to date for soft landing of mass-selected ions. A discussion of the competing processes that occur during ion deposition as well as the types of ions and surfaces that have been investigated follows in section 3. Section 4 discusses the physical phenomena that occur during and after ion soft landing including retention and reduction of ionic charge along with factors that impact the efficiency of ion deposition. The influence of soft landing on the secondary structure and biological activity of complex ions is addressed in section 5. Lastly, an overview of the structure and mobility as well as the catalytic, optical, magnetic, and redox properties of bare ionic clusters and nanoparticles deposited onto surfaces is presented in section 6.« less

The Zn12O12 cluster-assembled nanowires as a highly sensitive and selective gas sensor for NO and NO2.

PubMed

Yong, Yongliang; Su, Xiangying; Zhou, Qingxiao; Kuang, Yanmin; Li, Xiaohong

2017-12-13

Motivated by the recent realization of cluster-assembled nanomaterials as gas sensors, first-principles calculations are carried out to explore the stability and electronic properties of Zn 12 O 12 cluster-assembled nanowires and the adsorption behaviors of environmental gases on the Zn 12 O 12 -based nanowires, including CO, NO, NO 2 , SO 2 , NH 3 , CH 4 , CO 2 , O 2 and H 2 . Our results indicate that the ultrathin Zn 12 O 12 cluster-assembled nanowires are particularly thermodynamic stable at room temperature. The CO, NO, NO 2 , SO 2 , and NH 3 molecules are all chemisorbed on the Zn 12 O 12 -based nanowires with reasonable adsorption energies, but CH 4 , CO 2 , O 2 and H 2 molecules are only physically adsorbed on the nanowire. The electronic properties of the Zn 12 O 12 -based nanowire present dramatic changes after the adsorption of the NO and NO 2 molecules, especially their electric conductivity and magnetic properties, however, the other molecules adsorption hardly change the electric conductivity of the nanowire. Meanwhile, the recovery time of the nanowire sensor at T = 300 K is estimated at 1.5 μs and 16.7 μs for NO and NO 2 molecules, respectively. Furthermore, the sensitivities of NO and NO 2 are much larger than that of the other molecules. Our results thus conclude that the Zn 12 O 12 -based nanowire is a potential candidate for gas sensors with highly sensitivity for NO and NO 2 .

Super-resolution microscopy reveals the insulin-resistance-regulated reorganization of GLUT4 on plasma membranes.

PubMed

Gao, Lan; Chen, Junling; Gao, Jing; Wang, Hongda; Xiong, Wenyong

2017-01-15

GLUT4 (also known as SLC2A4) is essential for glucose uptake in skeletal muscles and adipocytes, which play central roles in whole-body glucose metabolism. Here, using direct stochastic optical reconstruction microscopy (dSTORM) to investigate the characteristics of plasma-membrane-fused GLUT4 at the single-molecule level, we have demonstrated that insulin and insulin resistance regulate the spatial organization of GLUT4 in adipocytes. Stimulation with insulin shifted the balance of GLUT4 on the plasma membrane toward a more dispersed configuration. In contrast, insulin resistance induced a more clustered distribution of GLUT4 and increased the mean number of molecules per cluster. Furthermore, our data demonstrate that the F 5 QQI motif and lipid rafts mediate the maintenance of GLUT4 clusters on the plasma membrane. Mutation of F 5 QQI (F 5 QQA-GLUT4) induced a more clustered distribution of GLUT4; moreover, destruction of lipid rafts in adipocytes expressing F 5 QQA-GLUT4 dramatically decreased the percentage of large clusters and the mean number of molecules per cluster. In conclusion, our data clarify the effects of insulin stimulation or insulin resistance on GLUT4 reorganization on the plasma membrane and reveal new pathogenic mechanisms of insulin resistance. © 2017. Published by The Company of Biologists Ltd.

Formation and Entrapment of Tris(8-hydroxyquinoline)aluminum from 8-Hydroxyquinoline in Anodic Porous Alumina

PubMed Central

Yamaguchi, Shohei; Matsui, Kazunori

2016-01-01

The formation and entrapment of tris(8-hydroxyquinoline)aluminum (Alq3) molecules on the surface of anodic porous alumina (APA) immersed in an ethanol solution of 8-hydroxyquinoline (HQ) were investigated by absorption, fluorescence, and Raman spectroscopies. The effects of the selected APA preparation conditions (galvanostatic or potentiostatic anodization method, anodizing current and voltage values, one- or two-step anodizing process, and sulfuric acid electrolyte concentration) on the adsorption and desorption of Alq3 species were examined. Among the listed parameters, sulfuric acid concentration was the most important factor in determining the Alq3 adsorption characteristics. The Alq3 content measured after desorption under galvanostatic conditions was 2.5 times larger than that obtained under potentiostatic ones, regardless of the adsorbed quantities. The obtained results suggest the existence of at least two types of adsorption sites on the APA surface characterized by different magnitudes of the Alq3 bonding strength. The related fluorescence spectra contained two peaks at wavelengths of 480 and 505 nm, which could be attributed to isolated Alq3 species inside nanovoids and aggregated Alq3 clusters in the pores of APA, respectively. The former species were attached to the adsorption sites with higher binding energies, whereas the latter ones were bound to the APA surface more weakly. Similar results were obtained for the Alq3 species formed from the HQ solution, which quantitatively exceeded the number of the Alq3 species adsorbed from the Alq3 solution. Alq3 molecules were formed in the HQ solution during the reaction of HQ molecules with the Al3+ ions in the oxide dissolution zone near the oxide/electrolyte interface through the cracks and the Al3+ ions adsorbed on surface of pore and cracks. In addition, it was suggested that HQ molecules could penetrate the nanovoids more easily than Alq3 species because of their smaller sizes, which resulted in higher magnitudes of the adsorption. PMID:28773840

Surface-enhanced Raman scattering on single-wall carbon nanotubes.

PubMed

Kneipp, Katrin; Kneipp, Harald; Dresselhaus, Mildred S; Lefrant, Serge

2004-11-15

Exploiting the effect of surface-enhanced Raman scattering (SERS), the Raman signal of single-wall carbon nanotubes (SWNTs) can be enhanced by up to 14 orders of magnitude when the tubes are in contact with silver or gold nanostructures and Raman scattering takes place predominantly in the enhanced local optical fields of the nanostructures. Such a level of enhancement offers exciting opportunities for ultrasensitive Raman studies on SWNTs and allows resonant and non-resonant Raman experiments to be done on single SWNTs at relatively high signal levels. Since the optical fields are highly localized within so-called "hot spots" on fractal silver colloidal clusters, lateral confinement of the Raman scattering can be as small as 5 nm, allowing spectroscopic selection of a single nanotube from a larger population. Moreover, since SWNTs are very stable "artificial molecules" with a high aspect ratio and a strong electron-phonon coupling, they are unique "test molecules" for investigating the SERS effect itself and for probing the "electromagnetic field contribution" and "charge transfer contribution" to the effect. SERS is also a powerful tool for monitoring the "chemical" interaction between the nanotube and the metal nanostructure.

Ab initio intermolecular potential energy surface for the CO2—N2 system and related thermophysical properties

NASA Astrophysics Data System (ADS)

Crusius, Johann-Philipp; Hellmann, Robert; Castro-Palacio, Juan Carlos; Vesovic, Velisa

2018-06-01

A four-dimensional potential energy surface (PES) for the interaction between a rigid carbon dioxide molecule and a rigid nitrogen molecule was constructed based on quantum-chemical ab initio calculations up to the coupled-cluster level with single, double, and perturbative triple excitations. Interaction energies for a total of 1893 points on the PES were calculated using the counterpoise-corrected supermolecular approach and basis sets of up to quintuple-zeta quality with bond functions. The interaction energies were extrapolated to the complete basis set limit, and an analytical site-site potential function with seven sites for carbon dioxide and five sites for nitrogen was fitted to the interaction energies. The CO2—N2 cross second virial coefficient as well as the dilute gas shear viscosity, thermal conductivity, and binary diffusion coefficient of CO2—N2 mixtures were calculated for temperatures up to 2000 K to validate the PES and to provide reliable reference values for these important properties. The calculated values are in very good agreement with the best experimental data.

Reactivity of commercially available monoclonal antibodies to human CD antigens with peripheral blood leucocytes of dromedary camels (Camelus dromedarius)

PubMed Central

Hussen, Jamal; Shawaf, Turke; Al-herz, Abdulkareem Imran; Alturaifi, Hussain R.; Alluwaimi, Ahmed M.

2017-01-01

Monoclonal antibodies (mAbs) to cell surface molecules have been proven as a key tool for phenotypic and functional characterization of the cellular immune response. One of the major difficulties in studying camel cellular immunity consists in the lack of mAbs that dtect their leukocyte differentiation antigens. In the present study two-parameter flow cytometry was used to screen existing commercially available mAbs to human leukocyte antigens and major histocompatibility molecules (MHC) for their reactivity with camel leukocytes. The comparison of patterns of reactivity obtained after labelling human and camel leukocytes have shown that mAbs specific to human cluster of differentiation (CD) 18, CD11a, CD11b and CD14 are predicted to be cross-reactive with homologous camel antigens. PMID:28652982

Molecular interaction of (ethanol)2-water heterotrimers.

PubMed

Mejía, Sol M; Espinal, Juan F; Restrepo, Albeiro; Mondragón, Fanor

2007-08-23

The potential energy surface of the (ethanol)2-water heterotrimers for the trans and gauche conformers of ethanol was studied using density functional theory. The same approximation was used for characterizing representative clusters of (ethanol)3, (methanol)3, and (methanol)2-water. Trimerization energies and enthalpies as well as the analysis of geometric parameters suggest that the structures with a cyclic pattern in the three hydrogen bonds of the type O-H---O (primary hydrogen bonds), where all molecules are proton donor-acceptor at the same time, are more stable than those with just two primary hydrogen bonds. Additionally, we propose the formation of "secondary hydrogen bonds" between hydrogen atoms of the methyl group of ethanol and the oxygen atom of water or other ethanol molecule (C-H---O), which were found to be weaker than the primary hydrogen bonds.

Cluster structures influenced by interaction with a surface.

PubMed

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.

Mass spectrometric and theoretical investigation of sulfate clusters in nanoscale water droplets

NASA Astrophysics Data System (ADS)

Lemke, K.

2017-12-01

The solvation of sulfate clusters of varying size and charge in water clusters and in nanoscale water droplets has been studied using electrospray ionization (ESI) FT-MS and density functional theory (DFT) molecular simulations. ESI mass spectra of solvated [Mg(MgSO4)m]2+(H2O)n with m≤10 and up to 15 water molecules have been recorded, and ion cluster experiments have been undertaken using a custom-modified FT-ICR mass spectrometer with the ability of IRMPD for ion dissociation. We present equilibrium geometries and energies for [Mg(MgSO4)m]2+(H2O)n, water-free and solvated with up to 100 water molecules, using swarm-based optimizers and DFT level calculations. Dominant cluster species identified following ESI of dilute (1-5 mM) MgSO4 solutions include hexa- and octa-nuclear magnesium sulfate ions, water-free and with a full first shell of water molecules. The largest clusters identified are magnesium sulfate decamers, i.e. [Mg(MgSO4)10]2+(H2O)n, with n≤15. As a very first step towards understanding the distribution and intensity of ESI ion mass spectra, we have identified the global minima of [Mg(MgSO4)m]2+(H2O)n with m≤10 and n≤100, and located likely global minima of magnesium sulfate clusters in the gas phase and in nano-scale water droplets. We will present a summary of the structural and energetic trends of solvated magnesium sulfate clusters, with a particular focus on structural transitions induced by cluster growth and solvation, the occurrence of "magic" number cluster species, their energetic properties and their potential role as atmospheric aqueous species.

Electronic spectra and excited-state dynamics of acridine and its hydrated clusters

NASA Astrophysics Data System (ADS)

Harthcock, Colin; Zhang, Jie; Kong, Wei; Mitsui, Masaaki; Ohshima, Yasuhiro

2017-04-01

We combine results from several different experiments to investigate the photophysics of acridine (Ac) and its hydrated clusters in the gas phase. Our findings are also compared with results from condensed phase studies. Similar to measurements of Ac dissolved in hydrocarbons, the lifetime of the first electronically excited state of isolated Ac in vacuum is too short for typical resonantly enhanced multiphoton ionization (REMPI) and laser induced fluorescence (LIF) experiments, hence no signal from REMPI and LIF can be attributed to monomeric Ac. Instead, sensitized phosphorescence emission spectroscopy is more successful in revealing the electronic states of Ac. Upon clustering with water, on the other hand, the lifetimes of the excited states are substantially increased to the nanosecond scale, and with two water molecules attached to Ac, the lifetime of the hydrated cluster is essentially the same as that of Ac in aqueous solutions. Detailed REMPI and ultraviolet-ultraviolet hole-burning experiments are then performed to reveal the structural information of the hydrated clusters. Although the formation of hydrogen bonds results in energy level reversal and energy separation between the first two excited states of Ac, its effect on the internal geometry of Ac is minimal, and all clusters with 1-3 water molecules demonstrate consistent intramolecular vibrational modes. Theoretical calculations reveal just one stable structure for each cluster under supersonic molecular beam conditions. Furthermore, different from mono- and di-water clusters, tri-water clusters consist of a linear chain of three water molecules attached to Ac. Consequently, the fragmentation pattern in the REMPI spectrum of tri-water clusters seems to be dominated by water trimer elimination, since the REMPI spectrum of Ac+.W3 is largely reproduced in the Ac+ mass channel, but not in the Ac+.W1 or Ac+.W2 channel.

Distal [FeS]-Cluster Coordination in [NiFe]-Hydrogenase Facilitates Intermolecular Electron Transfer

PubMed Central

Petrenko, Alexander; Stein, Matthias

2017-01-01

Biohydrogen is a versatile energy carrier for the generation of electric energy from renewable sources. Hydrogenases can be used in enzymatic fuel cells to oxidize dihydrogen. The rate of electron transfer (ET) at the anodic side between the [NiFe]-hydrogenase enzyme distal iron–sulfur cluster and the electrode surface can be described by the Marcus equation. All parameters for the Marcus equation are accessible from Density Functional Theory (DFT) calculations. The distal cubane FeS-cluster has a three-cysteine and one-histidine coordination [Fe4S4](His)(Cys)3 first ligation sphere. The reorganization energy (inner- and outer-sphere) is almost unchanged upon a histidine-to-cysteine substitution. Differences in rates of electron transfer between the wild-type enzyme and an all-cysteine mutant can be rationalized by a diminished electronic coupling between the donor and acceptor molecules in the [Fe4S4](Cys)4 case. The fast and efficient electron transfer from the distal iron–sulfur cluster is realized by a fine-tuned protein environment, which facilitates the flow of electrons. This study enables the design and control of electron transfer rates and pathways by protein engineering. PMID:28067774

Adsorption of Bromine on Gold Nanoclusters

NASA Astrophysics Data System (ADS)

Salvo, Christopher; Keagy, Josiah; Yarmoff, Jory

Small metal nanoclusters are extremely effective as catalysts, with rates that rival those of enzymes in biological systems. The first step in a catalytic reaction is the adsorption of a precursor molecule. The neutralization of alkali projectiles during low energy ion scattering (LEIS), which is acutely sensitive to the local electrostatic potential a few Å's above the surface, is used here to probe Au nanoclusters grown on SiO2 as they are reacted with Br2. Previous work had demonstrated very efficient neutralization in scattering from small catalytically active Au clusters, which was interpreted as an indication that the bare clusters are negatively charged. X-ray photoelectron spectroscopy and LEIS show little or no Br signal after exposing SiO2 and Au foil to Br2, suggesting that adsorption does not occur because the Br-Br bond does not break. Dissociative adsorption occurs rapidly, however, when small Au nanoclusters are reacted with Br2. 1.5 keV Na+ ions scattered from the Au clusters show a decrease in the neutralization probability as Br is reacted, indicating that adsorption results in charge being transferred from the cluster to the Br adatom. This material is based upon work supported by the National Science Foundation under CHE - 1611563.

H{sub 2} MOLECULAR CLUSTERS WITH EMBEDDED MOLECULES AND ATOMS AS THE SOURCE OF THE DIFFUSE INTERSTELLAR BANDS

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

Bernstein, L. S.; Clark, F. O.; Lynch, D. K., E-mail: larry@spectral.com, E-mail: dave@thulescientific.com

2013-05-01

We suggest that the diffuse interstellar bands (DIBs) arise from absorption lines of electronic transitions in molecular clusters primarily composed of a single molecule, atom, or ion ({sup s}eed{sup )}, embedded in a single-layer shell of H{sub 2} molecules. Less abundant variants of the cluster, including two seed molecules and/or a two-layer shell of H{sub 2} molecules, may also occur. The lines are broadened, blended, and wavelength-shifted by interactions between the seed and surrounding H{sub 2} shell. We refer to these clusters as contaminated H{sub 2} clusters (CHCs). We show that CHC spectroscopy matches the diversity of observed DIB spectralmore » profiles and provides good fits to several DIB profiles based on a rotational temperature of 10 K. CHCs arise from {approx}centimeter-sized, dirty H{sub 2} ice balls, called contaminated H{sub 2} ice macro-particles (CHIMPs), formed in cold, dense, giant molecular clouds (GMCs), and later released into the interstellar medium (ISM) upon GMC disruption. Attractive interactions, arising from Van der Waals and ion-induced dipole potentials, between the seeds and H{sub 2} molecules enable CHIMPs to attain centimeter-sized dimensions. When an ultraviolet (UV) photon is absorbed in the outer layer of a CHIMP, it heats the icy matrix and expels CHCs into the ISM. While CHCs are quickly destroyed by absorbing UV photons, they are replenished by the slowly eroding CHIMPs. Since CHCs require UV photons for their release, they are most abundant at, but not limited to, the edges of UV-opaque molecular clouds, consistent with the observed, preferred location of DIBs. An inherent property of CHCs, which can be characterized as nanometer size, spinning, dipolar dust grains, is that they emit in the radio-frequency region. We also show that the CHCs offer a natural explanation for the anomalous microwave emission feature in the {approx}10-100 GHz spectral region.« less

Self-assembled nanoparticle aggregates: Organizing disorder for high performance surface-enhanced spectroscopy

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

Fasolato, C.; Center for Life Nanoscience@Sapienza, Istituto Italiano di Tecnologia, Rome; Domenici, F., E-mail: fabiodomenici@gmail.com

2015-06-23

The coherent oscillations of the surface electron gas, known as surface plasmons, in metal nanostructures can give rise to the localization of intense electromagnetic fields at the metal-dielectric interface. These strong fields are exploited in surface enhanced spectroscopies, such as Surface Enhanced Raman Scattering (SERS), for the detection and characterization of molecules at very low concentration. Still, the implementation of SERS-based biosensors requires a high level of reproducibility, combined with cheap and simple fabrication methods. For this purpose, SERS substrates based on self-assembled aggregates of commercial metallic nanoparticles (Nps) can meet all the above requests. Following this line, we reportmore » on a combined micro-Raman and Atomic Force Microscopy (AFM) analysis of the SERS efficiency of micrometric silver Np aggregates (enhancement factors up to 10{sup 9}) obtained by self-assembly. Despite the intrinsic disordered nature of these Np clusters, we were able to sort out some general rules relating the specific aggregate morphology to its plasmonic response. We found strong evidences of cooperative effects among the NPs within the cluster and namely a clear dependence of the SERS-efficiency on both the cluster area (basically linear) and the number of stacked NPs layers. A cooperative action among the superimposed layers has been proved also by electromagnetic simulations performed on simplified nanostructures consisting of stacking planes of ordered Nps. Being clear the potentialities of these disordered self-assembled clusters, in terms of both easy fabrication and signal enhancement, we developed a specific nanofabrication protocol, based on electron beam lithography and molecular functionalization, that allowed for a fine control of the Np assemblies into designed shapes fixing their area and height. In particular, we fabricated 2D ordered arrays of disordered clusters choosing gold Nps owing to their high stability. AFM measurements confirmed the regularity in spacing and size (i.e. area and layer number) of the aggregates. Preliminary SERS measurements confirm the high signal enhancement and demonstrate a quite good reproducibility over large number of aggregates within 100×100 μm{sup 2} 2D super-structure. The availability of such a multisensor could allow a careful statistical analysis of the SERS response, thus leading to a reliable quantitative estimate of the presence of relevant molecular species even at ultra-low concentration.« less

Elucidation of Proton-Assisted Fluxionality in Transition-Metal Oxide Clusters

NASA Astrophysics Data System (ADS)

Ramabhadran, Raghunath O.; Mayhall, Nicholas J.; Becher, Edwin L. Becher, Iii; Chowdhury, Arefin; Raghavachari, Krishnan

2012-06-01

The phenomenon of fluxionality in the reactions of transition-metal oxide clusters provides many opportunities in various industrial and catalytic processes. We present an electronic structure investigation of the fluxionality pathways when anionic W3O6- and Mo3O6- clusters react with three small molecules - water, ammonia and hydrogen sulfide. The presentation features a detailed understanding of (a) how the fluxionality pathway occurs and (b) the various factors that affect the fluxionality pathway - such as the metal, different spin-states and the nature of the non-metal in the reacting small molecule.

Tuning the Emission and Quantum Yield of Gold and Silver Nanoclusters Through Ligand Design and Doping

NASA Astrophysics Data System (ADS)

Mishra, Dinesh

Nanoparticles have been extensively studied in the past few decades due to the possibilities they offer in applications ranging from medicine to energy generation. A new class of ultra-small noble metal nanoparticles consisting of tens to hundreds of atoms, commonly known as clusters or nanoclusters, have drawn interest of the research community recently due to their unique optical, electronic and structural properties. Over the past few years, advances have been made in the synthesis of atomically precise noble metal clusters (for example, silver and gold) with distinct optical properties. Their ultra-small size distinguishes them from conventional plasmonic nanoparticles and the properties are very sensitive to the slight variation in the compositon of the cluster, i.e. the number of the metal atoms and/or the nature of the ligands. These clusters are interesting because of their potential applications in field such as sensing, imaging, catalysis, clean energy, photonics, etc. as well as they provide fundamental insight into the evolution of the optical and electronic properties of these clusters. In this project, we explored the strategies to synthesize luminescent metallic clusters of gold and silver and to promote their solubility and stability in aqueous and biological medium. We focused particularly on the thiolate protected clusters due to the higher affinity of gold and silver to sulfur. Lipoic acid (Thioctic acid) is a bio-molecule with a cyclic disulfide ring, which also acts as a chelating ligand. Due to the higher binding affinity of the cyclic disulfide ring to nanocrystal surface, lipoic acid and chemically modified lipoic acid molecules have been widely reported for the synthesis and functionalization of inorganic nanocrystals. Here, we describe the use of bidentate lipoic acid ligands in the one phase growth of luminescent gold and silver nanoclusters. In addition, we have synthesized a new set of monothiol ligands containing PEG and zwitterion for the functionalization of fluorescent clusters. Chapter 1 introduces the fundamental properties of metallic clusters and the origin of these properties from electronic and structural point of view. The optical properties of ultra-small nanocrystals (<2 nm) in comparison to the plasmonic particles is described. In addition, the variation of optical and structural properties from one metal to another as well as one ligand to another is also compared. Chapter 2 describes the synthesis of ultra-small size gold clusters with different optical emission (ranging from blue to red) using photo-activated LA-PEG ligands. The influence of various factors on the growth of the clusters is also studied. Optical properties of the clusters were studied by UV-visible absorption, PL emission and excitation and time resolved fluorescence spectroscopy. XPS and DOSY NMR were used to characterize the oxidation states and sizes of these clusters. The photo-chemical transformation of LA-PEG ligands to thiols and the effect of various experimental parameters such as solvent, oxygen, ligand functional group and effect of acid are described in chapter 3. Thiol yield percentage was quantified using ellman assay. Chapter 4 describes the one phase aqueous synthesis of Ag29 clusters capped with bidentate dihydrolipoic acid (DHLA). We also describe the drastic enhancement of the PL intensity upon gold doping of the Ag29 clusters. Optical properties along with the size characterization by electrospray ionization mass spectrometry is also described. We further describe the growth of these clusters using DHLA-PEG molecules. Chapter 5 describes the synthesis of highly fluorescent Au25-xAgx clusters stabilized with two types of ligands (triphenylphosphine and thiols). We designed a set of monothiolate ligands appended with PEG and zwitterionic moieties. This approach allows to prepare water soluble and stable metallic clusters with enhanced photoluminescence and well defined optical properties. Chapter 6 is the overall summary of our findings and prospects and outlook.

Nucleation and island growth of alkanethiolate ligand domains on gold nanoparticles.

PubMed

Wang, Yifeng; Zeiri, Offer; Neyman, Alevtina; Stellacci, Francesco; Weinstock, Ira A

2012-01-24

The metal oxide cluster α-AlW(11)O(39)(9-) (1), readily imaged by cryogenic transmission electron microscopy (cryo-TEM), is used as a diagnostic protecting anion to investigate the self-assembly of alkanethiolate monolayers on electrostatically stabilized gold nanoparticles in water. Monolayers of 1 on 13.8 ± 0.9 nm diameter gold nanoparticles are displaced from the gold surface by mercaptoundecacarboxylate, HS(CH(2))(10)CO(2)(-) (11-MU). During this process, no aggregation is observed by UV-vis spectroscopy, and the intermediate ligand-shell organizations of 1 in cryo-TEM images indicate the presence of growing hydrophobic domains, or "islands", of alkanethiolates. UV-vis spectroscopic "titrations", based on changes in the surface plasmon resonance upon exchange of 1 by thiol, reveal that the 330 ± 30 molecules of 1 initially present on each gold nanoparticle are eventually replaced by 2800 ± 30 molecules of 11-MU. UV-vis kinetic data for 11-MU-monolayer formation reveal a slow phase, followed by rapid self-assembly. The Johnson, Mehl, Avrami, and Kolmogorov model gives an Avrami parameter of 2.9, indicating continuous nucleation and two-dimensional island growth. During nucleation, incoming 11-MU ligands irreversibly displace 1 from the Au-NP surface via an associative mechanism, with k(nucleation) = (6.1 ± 0.4) × 10(2) M(-1) s(-1), and 19 ± 8 nuclei, each comprised of ca. 8 alkanethiolates, appear on the gold-nanoparticle surface before rapid growth becomes kinetically dominant. Island growth is also first-order in [11-MU], and its larger rate constant, k(growth), (2.3 ± 0.2) × 10(4) M(-1) s(-1), is consistent with destabilization of molecules of 1 at the boundaries between the hydrophobic (alkanethiolate) and the electrostatically stabilized (inorganic) domains. © 2011 American Chemical Society

CO(2) incorporation in hydroxide and hydroperoxide containing water clusters--a unifying mechanism for hydrolysis and protolysis.

PubMed

Ryding, Mauritz J; Uggerud, Einar

2014-05-28

The reactions of CO2 with anionic water clusters containing hydroxide, OH(-)(H2O)n, and hydroperoxide, HO2(-)(H2O)n, have been studied in the isolated state using a mass spectrometric technique. The OH(-)(H2O)n clusters were found to react faster for n = 2,3, while for n >3 the HO2(-)(H2O)n clusters are more reactive. Insights from quantum chemical calculations revealed a common mechanism in which the decisive bicarbonate-forming step starts from a pre-reaction complex where OH(-) and CO2 are separated by one water molecule. Proton transfer from the water molecule to OH(-) then effectively moves the hydroxide ion motif next to the CO2 molecule. A new covalent bond is formed between CO2 and the emerging OH(-) in concert with the proton transfer. For larger clusters, successive proton transfers from H2O molecules to neighbouring OH(-) are required to effectively bring about the formation of the pre-reaction complex, upon which bicarbonate formation is accomplished according to the concerted mechanism. In this manner, a general mechanism is suggested, also applicable to bulk water and thereby to CO2 uptake in oceans. Furthermore, this mechanism avoids the intermediate H2CO3 by combining the CO2 hydrolysis step and the protolysis step into one. The general mechanistic picture is consistent with low enthalpy barriers and that the limiting factors are largely of entropic nature.

Single molecule analysis of B cell receptor motion during signaling activation

NASA Astrophysics Data System (ADS)

Rey Suarez, Ivan; Koo, Peter; Zhou, Shu; Wheatley, Brittany; Song, Wenxia; Mochrie, Simon; Upadhyaya, Arpita

B cells are an essential part of the adaptive immune system. They patrol the body for signs of infection in the form of antigen on the surface of antigen presenting cells. B cell receptor (BCR) binding to antigen induces a signaling cascade that leads to B cell activation and spreading. During activation, BCR form signaling microclusters that later coalesce as the cell contracts. We have studied the dynamics of BCRs on activated murine primary B cells using single particle tracking. The tracks are analyzed using perturbation expectation-maximization (pEM), a systems-level analysis, which allows identification of different short-time diffusive states from single molecule tracks. We identified four dominant diffusive states, two of which correspond to BCRs interacting with signaling molecules. For wild-type cells, the number of BCR in signaling states increases as the cell spreads and then decreases during cell contraction. In contrast, cells lacking the actin regulatory protein, N-WASP, are unable to contract and BCRs remain in the signaling states for longer times. These observations indicate that actin cytoskeleton dynamics modulate BCR diffusion and clustering. Our results provide novel information regarding the timescale of interaction between BCR and signaling molecules.

Glycogenomics as a mass spectrometry-guided genome-mining method for microbial glycosylated molecules.

PubMed

Kersten, Roland D; Ziemert, Nadine; Gonzalez, David J; Duggan, Brendan M; Nizet, Victor; Dorrestein, Pieter C; Moore, Bradley S

2013-11-19

Glycosyl groups are an essential mediator of molecular interactions in cells and on cellular surfaces. There are very few methods that directly relate sugar-containing molecules to their biosynthetic machineries. Here, we introduce glycogenomics as an experiment-guided genome-mining approach for fast characterization of glycosylated natural products (GNPs) and their biosynthetic pathways from genome-sequenced microbes by targeting glycosyl groups in microbial metabolomes. Microbial GNPs consist of aglycone and glycosyl structure groups in which the sugar unit(s) are often critical for the GNP's bioactivity, e.g., by promoting binding to a target biomolecule. GNPs are a structurally diverse class of molecules with important pharmaceutical and agrochemical applications. Herein, O- and N-glycosyl groups are characterized in their sugar monomers by tandem mass spectrometry (MS) and matched to corresponding glycosylation genes in secondary metabolic pathways by a MS-glycogenetic code. The associated aglycone biosynthetic genes of the GNP genotype then classify the natural product to further guide structure elucidation. We highlight the glycogenomic strategy by the characterization of several bioactive glycosylated molecules and their gene clusters, including the anticancer agent cinerubin B from Streptomyces sp. SPB74 and an antibiotic, arenimycin B, from Salinispora arenicola CNB-527.

Inhomogeneity Based Characterization of Distribution Patterns on the Plasma Membrane

PubMed Central

Paparelli, Laura; Corthout, Nikky; Wakefield, Devin L.; Sannerud, Ragna; Jovanovic-Talisman, Tijana; Annaert, Wim; Munck, Sebastian

2016-01-01

Cell surface protein and lipid molecules are organized in various patterns: randomly, along gradients, or clustered when segregated into discrete micro- and nano-domains. Their distribution is tightly coupled to events such as polarization, endocytosis, and intracellular signaling, but challenging to quantify using traditional techniques. Here we present a novel approach to quantify the distribution of plasma membrane proteins and lipids. This approach describes spatial patterns in degrees of inhomogeneity and incorporates an intensity-based correction to analyze images with a wide range of resolutions; we have termed it Quantitative Analysis of the Spatial distributions in Images using Mosaic segmentation and Dual parameter Optimization in Histograms (QuASIMoDOH). We tested its applicability using simulated microscopy images and images acquired by widefield microscopy, total internal reflection microscopy, structured illumination microscopy, and photoactivated localization microscopy. We validated QuASIMoDOH, successfully quantifying the distribution of protein and lipid molecules detected with several labeling techniques, in different cell model systems. We also used this method to characterize the reorganization of cell surface lipids in response to disrupted endosomal trafficking and to detect dynamic changes in the global and local organization of epidermal growth factor receptors across the cell surface. Our findings demonstrate that QuASIMoDOH can be used to assess protein and lipid patterns, quantifying distribution changes and spatial reorganization at the cell surface. An ImageJ/Fiji plugin of this analysis tool is provided. PMID:27603951

High-Resolution FRET Microscopy of Cholera Toxin B-Subunit and GPI-anchored Proteins in Cell Plasma Membranes

PubMed Central

Kenworthy, Anne K.; Petranova, Nadezda; Edidin, Michael

2000-01-01

“Lipid rafts” enriched in glycosphingolipids (GSL), GPI-anchored proteins, and cholesterol have been proposed as functional microdomains in cell membranes. However, evidence supporting their existence has been indirect and controversial. In the past year, two studies used fluorescence resonance energy transfer (FRET) microscopy to probe for the presence of lipid rafts; rafts here would be defined as membrane domains containing clustered GPI-anchored proteins at the cell surface. The results of these studies, each based on a single protein, gave conflicting views of rafts. To address the source of this discrepancy, we have now used FRET to study three different GPI-anchored proteins and a GSL endogenous to several different cell types. FRET was detected between molecules of the GSL GM1 labeled with cholera toxin B-subunit and between antibody-labeled GPI-anchored proteins, showing these raft markers are in submicrometer proximity in the plasma membrane. However, in most cases FRET correlated with the surface density of the lipid raft marker, a result inconsistent with significant clustering in microdomains. We conclude that in the plasma membrane, lipid rafts either exist only as transiently stabilized structures or, if stable, comprise at most a minor fraction of the cell surface. PMID:10793141

Adsorption of methanol, ethanol and water on well-characterized PtSn surface alloys

NASA Astrophysics Data System (ADS)

Panja, Chameli; Saliba, Najat; Koel, Bruce E.

1998-01-01

Adsorption and desorption of methanol (CH 3OH), ethanol (C 2H 5OH) and water on Pt(111) and two, ordered, PtSn alloys has been studied primarily using temperature-programmed desorption (TPD) mass spectroscopy. The two alloys studied were the {p(2 × 2) Sn}/{Pt(111) } and (√3 × √3) R30° {Sn}/{Pt(111) } surface alloys prepared by vapor deposition of Sn on Pt(111), with θSn = 0.25 and 0.33, respectively. All three molecules are weakly bonded and reversibly adsorbed under UHV conditions on all three surfaces, molecularly desorbing during TPD without any decomposition. The two PtSn surface alloys were found to chemisorb both methanol and ethanol slightly more weakly than on the Pt(111) surface. The desorption activation energies measured by TPD, and hence the adsorption energies, of both methanol and ethanol progressively decrease as the surface concentration of Sn increases, compared with Pt(111). The decreased binding energy leads one to expect a lower reactivity for these alcohols on the two alloys. The sticking coefficients and the monolayer coverages of these alcohols on the two alloys were identical to that on Pt(111) at 100 K, independent of the amount of Sn present in the surface layer. Alloying Sn in Pt(111) also slightly weakens the adsorption energy of water. Water clusters are formed even at low coverages on all three surfaces, eventually forming a water bilayer prior to the formation of a condensed ice phase. These results are relevant to a molecular-level explanation for the reactivity of Sn-promoted Pt surfaces that have been used in the electro-oxidation of simple organic molecules.

Feature extraction using molecular planes for fuzzy relational clustering of a flexible dopamine reuptake inhibitor.

PubMed

Banerjee, Amit; Misra, Milind; Pai, Deepa; Shih, Liang-Yu; Woodley, Rohan; Lu, Xiang-Jun; Srinivasan, A R; Olson, Wilma K; Davé, Rajesh N; Venanzi, Carol A

2007-01-01

Six rigid-body parameters (Shift, Slide, Rise, Tilt, Roll, Twist) are commonly used to describe the relative displacement and orientation of successive base pairs in a nucleic acid structure. The present work adapts this approach to describe the relative displacement and orientation of any two planes in an arbitrary molecule-specifically, planes which contain important pharmacophore elements. Relevant code from the 3DNA software package (Nucleic Acids Res. 2003, 31, 5108-5121) was generalized to treat molecular fragments other than DNA bases as input for the calculation of the corresponding rigid-body (or "planes") parameters. These parameters were used to construct feature vectors for a fuzzy relational clustering study of over 700 conformations of a flexible analogue of the dopamine reuptake inhibitor, GBR 12909. Several cluster validity measures were used to determine the optimal number of clusters. Translational (Shift, Slide, Rise) rather than rotational (Tilt, Roll, Twist) features dominate clustering based on planes that are relatively far apart, whereas both types of features are important to clustering when the pair of planes are close by. This approach was able to classify the data set of molecular conformations into groups and to identify representative conformers for use as template conformers in future Comparative Molecular Field Analysis studies of GBR 12909 analogues. The advantage of using the planes parameters, rather than the combination of atomic coordinates and angles between molecular planes used in our previous fuzzy relational clustering of the same data set (J. Chem. Inf. Model. 2005, 45, 610-623), is that the present clustering results are independent of molecular superposition and the technique is able to identify clusters in the molecule considered as a whole. This approach is easily generalizable to any two planes in any molecule.

Accurate Construction of Photoactivated Localization Microscopy (PALM) Images for Quantitative Measurements

PubMed Central

Coltharp, Carla; Kessler, Rene P.; Xiao, Jie

2012-01-01

Localization-based superresolution microscopy techniques such as Photoactivated Localization Microscopy (PALM) and Stochastic Optical Reconstruction Microscopy (STORM) have allowed investigations of cellular structures with unprecedented optical resolutions. One major obstacle to interpreting superresolution images, however, is the overcounting of molecule numbers caused by fluorophore photoblinking. Using both experimental and simulated images, we determined the effects of photoblinking on the accurate reconstruction of superresolution images and on quantitative measurements of structural dimension and molecule density made from those images. We found that structural dimension and relative density measurements can be made reliably from images that contain photoblinking-related overcounting, but accurate absolute density measurements, and consequently faithful representations of molecule counts and positions in cellular structures, require the application of a clustering algorithm to group localizations that originate from the same molecule. We analyzed how applying a simple algorithm with different clustering thresholds (tThresh and dThresh) affects the accuracy of reconstructed images, and developed an easy method to select optimal thresholds. We also identified an empirical criterion to evaluate whether an imaging condition is appropriate for accurate superresolution image reconstruction with the clustering algorithm. Both the threshold selection method and imaging condition criterion are easy to implement within existing PALM clustering algorithms and experimental conditions. The main advantage of our method is that it generates a superresolution image and molecule position list that faithfully represents molecule counts and positions within a cellular structure, rather than only summarizing structural properties into ensemble parameters. This feature makes it particularly useful for cellular structures of heterogeneous densities and irregular geometries, and allows a variety of quantitative measurements tailored to specific needs of different biological systems. PMID:23251611

Exciton Splitting of Adsorbed and Free 4-Nitroazobenzene Dimers: A Quantum Chemical Study.

PubMed

Titov, Evgenii; Saalfrank, Peter

2016-05-19

Molecular photoswitches such as azobenzenes, which undergo photochemical trans ↔ cis isomerizations, are often mounted for possible applications on a surface and/or surrounded by other switches, for example, in self-assembled monolayers. This may suppress the isomerization cross section due to possible steric reasons, or, as recently speculated, by exciton coupling to neighboring switches, leading to ultrafast electronic quenching (Gahl et al., J. Am. Chem. Soc. 2010, 132, 1831). The presence of exciton coupling has been anticipated from a blue shift of the optical absorption band, compared to molecules in solution. From the theory side the need arises to properly analyze and quantify the change of absorption spectra of interacting and adsorbed switches. In particular, suitable methods should be identified, and effects of intermolecule and molecule-surface interactions on spectra should be disentangled. In this paper by means of time-dependent Hartree-Fock (TD-HF), various flavors of time-dependent density functional theory (TD-DFT), and the correlated wave function based coupled-cluster (CC2) method we investigated the 4-nitroazobenzene molecule as an example: The low-lying singlet excited states in the isolated trans monomer and dimer as well as their composites with a silicon pentamantane nanocluster, which serves also as a crude model for a silicon surface, were determined. As most important results we found that (i) HF, CC2, range-separated density functionals, or global hybrids with large amount of exact exchange are able to describe exciton (Davydov) splitting properly, while hybrids with small amount of exact exchange fail producing spurious charge transfer. (ii) The exciton splitting in a free dimer would lead to a blue shift of the absorption signal; however, this effect is almost nullified or even overcompensated by the shift arising from van der Waals interactions between the two molecules. (iii) Adsorption on the Si "surface" leads to a further, strong red shift for the present system. (iv) At a next-nearest neighbor distance (of ∼3.6 Å), the exciton splitting is ∼0.3 eV, with or without "surface", suggesting a rapid quenching of the molecular π → π* excitation. At larger distances, exciton splitting decreases rapidly.

Atomistic investigation on the detachment of oil molecules from defective alumina surface

NASA Astrophysics Data System (ADS)

Xie, W. K.; Sun, Y. Z.; Liu, H. T.

2017-12-01

The mechanism of oil detachment from defective alumina surface in aqueous solution was investigated via atomistic molecular dynamics (MD) simulations. Special attention was focused on the effect of surface defect on the oil detachment. Our simulation results suggest that compared with perfect Al2O3 surface, defective substrate surface provides much more sites for the adsorption of oil molecules, thus it has higher oil adsorption energy. However, higher oil-solid adsorption energy does not mean that oil contaminants are much more difficult to be detached. It is found that surface defect could induce the spontaneous imbibition of water molecules, effectively promoting the detachment of oil molecules. Thus, compared with perfect alumina surface, the detachment of oil molecules from defective alumina surface tends to be much easier. Moreover, surface defect could lead to the oil residues inside surface defect. In water solution, the entire detachment process of oil molecules on defective surface consists of following stages, including the early detachment of oil molecules inside surface defect induced by capillary-driven spontaneous imbibition of water molecules, the following conformational change of oil molecules on topmost surface and the final migration of detached oil molecules from solid surface. These findings may help to sufficiently enrich the removal mechanism of oil molecules adhered onto defective solid surface.

Spin-symmetry conversion and internal rotation in high J molecular systems

NASA Astrophysics Data System (ADS)

Mitchell, Justin; Harter, William

2006-05-01

Dynamics and spectra of molecules with internal rotation or rovibrational coupling is approximately modeled by rigid or semi-rigid rotors with attached gyroscopes. Using Rotational Energy (RE)^1 surfaces, high resolution molecular spectra for high angular momentum show two distinct but related phenomena; spin-symmetry conversion and internal rotation. For both cases the high total angular momentum allows for transitions that would otherwise be forbidden. Molecular body-frame J-localization effects associated with tight energy level-clusters dominate the rovibronic spectra of high symmetry molecules, particularly spherical tops at J>10. ^2 The effects include large and widespread spin-symmetry mixing contrary to conventional wisdom^3 about weak nuclear moments. Such effects are discussed showing how RE surface plots may predict them even at low J. Classical dynamics of axially constrained rotors are approximated by intersecting rotational-energy-surfaces (RES) that have (J-S).B.(J-S) forms in the limit of constraints that do no work. Semi-classical eigensolutions are compared to those found by direct diagonalization. ^1 W.G Hater, in Handbook of Atomic, Molecular and Optical Physics, edited by G.W.F Drake (Springer, Germany 2006) ^2 W. G. Harter, Phys. Rev. A24,192-262(1981). ^3 G. Herzberg, Infrared and Raman Spectra (VanNostrand 1945) pp. 458,463.

Early Dynamics and Stabilization Mechanisms of Oil-in-Water Emulsions Containing Colloidal Particles Modified with Short Amphiphiles: A Numerical Study.

PubMed

Cerbelaud, Manuella; Videcoq, Arnaud; Alison, Lauriane; Tervoort, Elena; Studart, André R

2017-12-19

Emulsions stabilized by mixtures of particles and amphiphilic molecules are relevant for a wide range of applications, but their dynamics and stabilization mechanisms on the colloidal level are poorly understood. Given the challenges to experimentally probe the early dynamics and mechanisms of droplet stabilization, Brownian dynamics simulations are developed here to study the behavior of oil-in-water emulsions stabilized by colloidal particles modified with short amphiphiles. Simulation parameters are based on an experimental system that consists of emulsions obtained with octane as the oil phase and a suspension of alumina colloidal particles modified with short carboxylic acids as the continuous aqueous medium. The numerical results show that attractive forces between the colloidal particles favor the formation of closely packed clusters on the droplet surface or of a percolating network of particles throughout the continuous phase, depending on the amphiphile concentration. Simulations also reveal the importance of a strong adsorption of particles at the liquid interface to prevent their depletion from the droplet surface when another droplet approaches. Strongly adsorbed particles remain immobile on the droplet surface, generating an effective steric barrier against droplet coalescence. These findings provide new insights into the early dynamics and mechanisms of stabilization of emulsions using particles and amphiphilic molecules.

Enzyme microheterogeneous hydration and stabilization in supercritical carbon dioxide.

PubMed

Silveira, Rodrigo L; Martínez, Julian; Skaf, Munir S; Martínez, Leandro

2012-05-17

Supercritical carbon dioxide is a promising green-chemistry solvent for many enzyme-catalyzed chemical reactions, yet the striking stability of some enzymes in such unconventional environments is not well understood. Here, we investigate the stabilization of the Candida antarctica Lipase B (CALB) in supercritical carbon dioxide-water biphasic systems using molecular dynamics simulations. The preservation of the enzyme structure and optimal activity depend on the presence of small amounts of water in the supercritical dispersing medium. When the protein is at least partially hydrated, water molecules bind to specific sites on the enzyme surface and prevent carbon dioxide from penetrating its catalytic core. Strikingly, water and supercritical carbon dioxide cover the protein surface quite heterogeneously. In the first solvation layer, the hydrophilic residues at the surface of the protein are able to pin down patches of water, whereas carbon dioxide solvates preferentially hydrophobic surface residues. In the outer solvation shells, water molecules tend to cluster predominantly on top of the larger water patches of the first solvation layer instead of spreading evenly around the remainder of the protein surface. For CALB, this exposes the substrate-binding region of the enzyme to carbon dioxide, possibly facilitating diffusion of nonpolar substrates into the catalytic funnel. Therefore, by means of microheterogeneous solvation, enhanced accessibility of hydrophobic substrates to the active site can be achieved, while preserving the functional structure of the enzyme. Our results provide a molecular picture on the nature of the stability of proteins in nonaqueous media.

Alkali-ion microsolvation with benzene molecules.

PubMed

Marques, J M C; Llanio-Trujillo, J L; Albertí, M; Aguilar, A; Pirani, F

2012-05-24

The target of this investigation is to characterize by a recently developed methodology, the main features of the first solvation shells of alkaline ions in nonpolar environments due to aromatic rings, which is of crucial relevance to understand the selectivity of several biochemical phenomena. We employ an evolutionary algorithm to obtain putative global minima of clusters formed with alkali-ions (M(+)) solvated with n benzene (Bz) molecules, i.e., M(+)-(Bz)(n). The global intermolecular interaction has been decomposed in Bz-Bz and in M(+)-Bz contributions, using a potential model based on different decompositions of the molecular polarizability of benzene. Specifically, we have studied the microsolvation of Na(+), K(+), and Cs(+) with benzene molecules. Microsolvation clusters up to n = 21 benzene molecules are involved in this work and the achieved global minimum structures are reported and discussed in detail. We observe that the number of benzene molecules allocated in the first solvation shell increases with the size of the cation, showing three molecules for Na(+) and four for both K(+) and Cs(+). The structure of this solvation shell keeps approximately unchanged as more benzene molecules are added to the cluster, which is independent of the ion. Particularly stable structures, so-called "magic numbers", arise for various nuclearities of the three alkali-ions. Strong "magic numbers" appear at n = 2, 3, and 4 for Na(+), K(+), and Cs(+), respectively. In addition, another set of weaker "magic numbers" (three per alkali-ion) are reported for larger nuclearities.

Interaction of size-selected gold nanoclusters with dopamine

NASA Astrophysics Data System (ADS)

Montone, Georgia R.; Hermann, Eric; Kandalam, Anil K.

2016-12-01

We present density functional theory based results on the interaction of size-selected gold nanoclusters, Au10 and Au20, with dopamine molecule. The gold clusters interact strongly with the nitrogen site of dopamine, thereby forming stable gold-dopamine complexes. Our calculations further show that there is no site specificity on the planar Au10 cluster with all the edge gold atoms equally preferred. On the other hand, in the pyramidal Au20 cluster, the vertex metal atom is the most active site. As the size increased from Au10 to Au20, the interaction strength has shown a declining trend. The effect of aqueous environment on the interaction strengths were also studied by solvation model. It is found that the presence of solvent water stabilizes the interaction between the metal cluster and dopamine molecule, even though for Au10 cluster the energy ordering of the isomers changed from that of the gas-phase.

Vibrational Spectroscopy of BENZENE-(WATER)_N Clusters with N=6,7

NASA Astrophysics Data System (ADS)

Tabor, Daniel P.; Sibert, Edwin; Kusaka, Ryoji; Walsh, Patrick S.; Zwier, Timothy S.

2015-06-01

The investigation of benzene-water clusters (Bz-(H_2O)_n) provides insight into the relative importance π-hydrogen bond interactions in cluster formation. Taking advantage of the higher resolution of current IR sources, isomer-specific resonant ion-dip infrared (RIDIR) spectra were recorded in the OH stretch region (3000-3750 cm-1). A local mode Hamiltonian for describing the OH stretch vibrations of water clusters is applied to Bz-(H_2O)_6 and Bz-(H_2O)_7 and compared with the RIDIR spectra. These clusters are the smallest water clusters in which three-dimensional H-bonded networks containing three-coordinate water molecules begin to be formed, and are therefore particularly susceptible to re-ordering or re-shaping in response to the presence of a benzene molecule. The spectrum of Bz-(H_2O)_6 is assigned to an inverted book structure while the major conformer of Bz-(H_2O)_7 is assigned to an S_4-derived inserted cubic structure in which the benzene occupies one corner of the cube. The local mode model is used to extract monomer Hamiltonians for individual water molecules, including stretch-bend Fermi resonance and intra-monomer couplings. The monomer Hamiltonians divide into sub-groups based on their local H-bonding architecture (DA, DDA, DAA) and the nature of their interaction with benzene.

Nano-confinement inside molecular metal oxide clusters: Dynamics and modified encapsulation behavior

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

Wang, Zhe; Daemen, Luke L.; Cheng, Yongqiang

Encapsulation behavior, as well as the presence of internal catalytically-active sites, has been spurring the applications of a 3 nm hollow spherical metal oxide cluster {Mo 132} as an encapsulation host and a nano-reactor. Due to its well-defined and tunable cluster structures, and nano-scaled internal void space comparable to the volumes of small molecules, this cluster provides a good model to study the dynamics of materials under ultra-confinement. Neutron scattering studies suggest that bulky internal ligands inside the cluster show slower and limited dynamics compared to their counterparts in the bulk state, revealing the rigid nature of the skeleton ofmore » the internal ligands. Furthermore, NMR studies indicate that the rigid internal ligands that partially cover the interfacial pore on the molybdenum oxide shells are able to block some large guest molecules from going inside the capsule cluster, which provides a convincing protocol for size-selective encapsulation and separation.« less

Nano-confinement inside molecular metal oxide clusters: Dynamics and modified encapsulation behavior

DOE PAGES

Wang, Zhe; Daemen, Luke L.; Cheng, Yongqiang; ...

2016-08-19

Encapsulation behavior, as well as the presence of internal catalytically-active sites, has been spurring the applications of a 3 nm hollow spherical metal oxide cluster {Mo 132} as an encapsulation host and a nano-reactor. Due to its well-defined and tunable cluster structures, and nano-scaled internal void space comparable to the volumes of small molecules, this cluster provides a good model to study the dynamics of materials under ultra-confinement. Neutron scattering studies suggest that bulky internal ligands inside the cluster show slower and limited dynamics compared to their counterparts in the bulk state, revealing the rigid nature of the skeleton ofmore » the internal ligands. Furthermore, NMR studies indicate that the rigid internal ligands that partially cover the interfacial pore on the molybdenum oxide shells are able to block some large guest molecules from going inside the capsule cluster, which provides a convincing protocol for size-selective encapsulation and separation.« less

Involvement of glycosphingolipid-enriched lipid rafts in inflammatory responses.

PubMed

Iwabuchi, Kazuhisa

2015-01-01

Glycosphingolipids (GSLs) are membrane components consisting of hydrophobic ceramide and hydrophilic sugar moieties. GSLs cluster with cholesterol in cell membranes to form GSL-enriched lipid rafts. Biochemical analyses have demonstrated that GSL-enriched lipid rafts contain several kinds of transducer molecules, including Src family kinases. Among the GSLs, lactosylceramide (LacCer, CDw17) can bind to various microorganisms, is highly expressed on the plasma membranes of human phagocytes, and forms lipid rafts containing the Src family tyrosine kinase Lyn. LacCer-enriched lipid rafts mediate immunological and inflammatory reactions, including superoxide generation, chemotaxis, and non-opsonic phagocytosis. Therefore, LacCer-enriched membrane microdomains are thought to function as pattern recognition receptors (PRRs), which recognize pathogen-associated molecular patterns (PAMPs) expressed on microorganisms. LacCer also serves as a signal transduction molecule for functions mediated by CD11b/CD18-integrin (αM/β2-integrin, CR3, Mac-1), as well as being associated with several key cellular processes. LacCer recruits PCKα/ε and phospholipase A2 to stimulate PECAM-1 expression in human monocytes and their adhesion to endothelial cells, as well as regulating β1-integrin clustering and endocytosis on cell surfaces. This review describes the organizational and inflammation-related functions of LacCer-enriched lipid rafts.

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

Hou, Gao-Lei; Lin, Wei; Deng, Shihu

Recent lab and field measurements have indicated critical roles of organic acids in enhancing new atmospheric aerosol formation. Such findings have stimulated theoretical studies with the aim of understanding interaction of organic acids with common aerosol nucleation precursors like bisulfate (HSO4-). In this Letter, we report a combined negative ion photoelectron spectroscopic and theoretical investigation of molecular clusters formed by HSO4- with succinic acid (SUA, HO2C(CH2)2CO2H), HSO4-(SUA)n (n = 0-2), along with HSO4-(H2O)n and HSO4-(H2SO4)n. It is found that one SUA molecule can stabilize HSO4- by ca. 39 kcal/mol, triple the corresponding value that one water molecule is capable ofmore » (ca. 13 kcal/mol). Molecular dynamics simulations and quantum chemical calculations reveal the most plausible structures of these clusters and attribute the stability of these clusters due to formation of strong hydrogen bonds. This work provides direct experimental evidence showing significant thermodynamic advantage by involving organic acid molecules to promote formation and growth in bisulfate clusters and aerosols.« less

Defining the membrane disruption mechanism of kalata B1 via coarse-grained molecular dynamics simulations

PubMed Central

Nawae, Wanapinun; Hannongbua, Supa; Ruengjitchatchawalya, Marasri

2014-01-01

Kalata B1 has been demonstrated to have bioactivity relating to membrane disruption. In this study, we conducted coarse-grained molecular dynamics simulations to gain further insight into kB1 bioactivity. The simulations were performed at various concentrations of kB1 to capture the overall progression of its activity. Two configurations of kB1 oligomers, termed tower-like and wall-like clusters, were detected. The conjugation between the wall-like oligomers resulted in the formation of a ring-like hollow in the kB1 cluster on the membrane surface. Our results indicated that the molecules of kB1 were trapped at the membrane-water interface. The interfacial membrane binding of kB1 induced a positive membrane curvature, and the lipids were eventually extracted from the membrane through the kB1 ring-like hollow into the space inside the kB1 cluster. These findings provide an alternative view of the mechanism of kB1 bioactivity that corresponds with the concept of an interfacial bioactivity model. PMID:24492660

Laser trapping-induced crystallization of L-phenylalanine through its high-concentration domain formation.

PubMed

Yuyama, Ken-ichi; Wu, Chi-Shiun; Sugiyama, Teruki; Masuhara, Hiroshi

2014-02-01

We present the laser trapping-induced crystallization of L-phenylalanine through high-concentration domain formation in H2O and D2O solutions which is achieved by focusing a continuous-wave (CW) near-infrared laser beam at the solution surface. Upon laser irradiation into the H2O solution, laser trapping of the liquid-like clusters increases the local concentration, accompanying laser heating, and a single plate-like crystal is eventually prepared at the focal spot. On the other hand, in the D2O solution, a lot of the monohydrate needle-like crystals are observed, not at the focal spot where the concentration is high enough to trigger crystal nucleation, but in the 0.5-1.5 mm range from the focal spot. The dynamics and mechanism of the amazing crystallization behaviour induced by laser trapping are discussed from the viewpoints of the concentration increase due to laser heating depending on solvent, the large high-concentration domain formation by laser trapping of liquid-like clusters, and the orientational disorder of molecules/clusters at the domain edge.

Theoretical research program to study chemical reactions in AOTV bow shock tubes

NASA Technical Reports Server (NTRS)

Taylor, Peter

1992-01-01

Effort continued through this period to refine and expand the SIRIUS/ABACUS program package for CASSCF and RASSCF second derivatives. A new approach to computing the Gaussian integral derivatives that require much of the time in gradient and Hessian calculations was devised. Several different studies were undertaken in the area of application calculations. These include a study of proton transfer in the HF trimer, which provides an analog of rearrangement reactions, and the extension of our previous work on Be and Mg clusters to Ca clusters. In addition, a very accurate investigation of the lowest-lying potential curves of the O2 molecule was completed. These curves are essential for evaluating different models of the terrestrial atmosphere nightglow. The most effort this year was devoted to a large scale investigation of stationary points on the C4H4 surface, and the thermochemistry of acetylene/acetylene reaction.

N2O reduction over a fullerene-like boron nitride nanocage: A DFT study

NASA Astrophysics Data System (ADS)

Esrafili, Mehdi D.

2017-07-01

We study, for the first time, the adsorption and catalytic decomposition of N2O molecule over a fullerene-like boron nitride nanocage (B12N12) using density functional theory calculations. It is found that the electron donating property of the cage plays an important role in the adsorption and activation of N2O. By the incorporation of a carbon atom into B12N12 cluster, our results indicate that the adsorption of N2O over B11N12C or B12N11C is more stronger than over pristine B12N12. The decomposition of N2O into N2 and O species over the C-doped clusters is energetically more favorable than that on B12N12. Moreover, the C-doping plays an important role in reducing the activation barrier for the CO + O* reaction over B12N12 surface.

The spherical-harmonics representation for the interaction between diatomic molecules: The general case and applications to COsbnd CO and COsbnd HF

NASA Astrophysics Data System (ADS)

Barreto, Patricia R. P.; Cruz, Ana Claudia P. S.; Barreto, Rodrigo L. P.; Palazzetti, Federico; Albernaz, Alessandra F.; Lombardi, Andrea; Maciel, Glauciete S.; Aquilanti, Vincenzo

2017-07-01

The spherical-harmonics expansion is a mathematically rigorous procedure and a powerful tool for the representation of potential energy surfaces of interacting molecular systems, determining their spectroscopic and dynamical properties, specifically in van der Waals clusters, with applications also to classical and quantum molecular dynamics simulations. The technique consists in the construction (by ab initio or semiempirical methods) of the expanded potential interaction up to terms that provide the generation of a number of leading configurations sufficient to account for faithful geometrical representations. This paper reports the full general description of the method of the spherical-harmonics expansion as applied to diatomic-molecule - diatomic-molecule systems of increasing complexity: the presentation of the mathematical background is given for providing both the application to the prototypical cases considered previously (O2sbnd O2, N2sbnd N2, and N2sbnd O2 systems) and the generalization to: (i) the COsbnd CO system, where a characteristic feature is the lower symmetry order with respect to the cases studied before, requiring a larger number of expansion terms necessary to adequately represent the potential energy surface; and (ii) the COsbnd HF system, which exhibits the lowest order of symmetry among this class of aggregates and therefore the highest number of leading configurations.

Enhanced EGFR Targeting Activity of Plasmonic Nanostructures with Engineered GE11 Peptide.

PubMed

Biscaglia, Francesca; Rajendran, Senthilkumar; Conflitti, Paolo; Benna, Clara; Sommaggio, Roberta; Litti, Lucio; Mocellin, Simone; Bocchinfuso, Gianfranco; Rosato, Antonio; Palleschi, Antonio; Nitti, Donato; Gobbo, Marina; Meneghetti, Moreno

2017-12-01

Plasmonic nanostructures show important properties for biotechnological applications, but they have to be guided on the target for exploiting their potentialities. Antibodies are the natural molecules for targeting. However, their possible adverse immunogenic activity and their cost have suggested finding other valid substitutes. Small molecules like peptides can be an alternative source of targeting agents, even if, as single molecules, their binding affinity is usually not very good. GE11 is a small dodecapeptide with specific binding to the epidermal growth factor receptor (EGFR) and low immunogenicity. The present work shows that thousands of polyethylene glycol (PEG) chains modified with lysines and functionalized with GE11 on clusters of naked gold nanoparticles, obtained by laser ablation in water, achieves a better targeting activity than that recorded with nanoparticles decorated with the specific anti-EGFR antibody Cetuximab (C225). The insertion of the cationic spacer between the polymeric part of the ligand and the targeting peptide allows for a proper presentation of GE11 on the surface of the nanosystems. Surface enhanced resonance Raman scattering signals of the plasmonic gold nanoparticles are used for quantifying the targeting activity. Molecular dynamic calculations suggest that subtle differences in the exposition of the peptide on the PEG sea are important for the targeting activity. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analysing and Navigating Natural Products Space for Generating Small, Diverse, But Representative Chemical Libraries.

PubMed

O'Hagan, Steve; Kell, Douglas B

2018-01-01

Armed with the digital availability of two natural products libraries, amounting to some 195 885 molecular entities, we ask the question of how we can best sample from them to maximize their "representativeness" in smaller and more usable libraries of 96, 384, 1152, and 1920 molecules. The term "representativeness" is intended to include diversity, but for numerical reasons (and the likelihood of being able to perform a QSAR) it is necessary to focus on areas of chemical space that are more highly populated. Encoding chemical structures as fingerprints using the RDKit "patterned" algorithm, we first assess the granularity of the natural products space using a simple clustering algorithm, showing that there are major regions of "denseness" but also a great many very sparsely populated areas. We then apply a "hybrid" hierarchical K-means clustering algorithm to the data to produce more statistically robust clusters from which representative and appropriate numbers of samples may be chosen. There is necessarily again a trade-off between cluster size and cluster number, but within these constraints, libraries containing 384 or 1152 molecules can be found that come from clusters that represent some 18 and 30% of the whole chemical space, with cluster sizes of, respectively, 50 and 27 or above, just about sufficient to perform a QSAR. By using the online availability of molecules via the Molport system (www.molport.com), we are also able to construct (and, for the first time, provide the contents of) a small virtual library of available molecules that provided effective coverage of the chemical space described. Consistent with this, the average molecular similarities of the contents of the libraries developed is considerably smaller than is that of the original libraries. The suggested libraries may have use in molecular or phenotypic screening, including for determining possible transporter substrates. © 2017 The Authors. Biotechnology Journal Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Mass analysis of neutral particles and ions released during electrical breakdowns on spacecraft surfaces

NASA Technical Reports Server (NTRS)

Kendall, B. R. F.

1983-01-01

A specialized spectrometer was designed and developed to measure the mass and velocity distributions of neutral particles (molecules and molecular clusters) released from metal-backed Teflon and Kapton films. Promising results were obtained with an insulation breakdown initiation system based on a moveable contact touching the insulated surfaces. A variable energy, high voltage pulse is applied to the contact. The resulting surface damage sites can be made similar in size and shape to those produced by a high voltage electron beam system operating at similar discharge energies. The point discharge apparatus was used for final development of several high speed recording systems and for measurements of the composition of the materials given off by the discharge. Results with this apparatus show evolution of large amounts of fluorocarbon fragments from discharge through Teflon FEP, while discharges through Kapton produce mainly very light hydrocarbon fragments at masses below about 80 a.m.u.

Giant Spherical Cluster with I-C140 Fullerene Topology**

PubMed Central

Heinl, Sebastian; Peresypkina, Eugenia; Sutter, Jörg; Scheer, Manfred

2015-01-01

We report on an effective cluster expansion of CuBr-linked aggregates by the increase of the steric bulk of the CpR ligand in the pentatopic molecules [CpRFe(η5-P5)]. Using [CpBIGFe(η5-P5)] (CpBIG=C5(4-nBuC6H4)5), the novel multishell aggregate [{CpBIGFe(η5:2:1:1:1:1:1-P5)}12(CuBr)92] is obtained. It shows topological analogy to the theoretically predicted I-C140 fullerene molecule. The spherical cluster was comprehensively characterized by various methods in solution and in the solid state. PMID:26411255

Metal-atom Interactions and Clustering in Organic Semiconductor Systems

NASA Astrophysics Data System (ADS)

Tomita, Yoko; Park, Tea-uk; Nakayama, Takashi

2017-07-01

The interatomic interactions and clustering of metal atoms have been studied by first-principles calculations in graphene, pentacene, and polyacetylene as representative organic systems. It is shown that long-range repulsive Coulomb interaction appears between metal atoms with small electronegativity such as Al due to their ionization on host organic molecules, inducing their scattered distribution in organic systems. On the other hand, metal atoms with large electronegativity such as Au are weakly bonded to organic molecules, easily diffuse in molecular solids, and prefer to combine with each other owing to their short-range strong metallic-bonding interaction, promoting metal cluster generation in organic systems.

Dynamics of ions in a water drop using the AMOEBA polarizable force field

NASA Astrophysics Data System (ADS)

Thaunay, Florian; Ohanessian, Gilles; Clavaguéra, Carine

2017-03-01

Various ions carrying a charge from -2 to +3 were confined in a drop of 100 water molecules as a way to model coordination properties inside the cluster and at the interface. The behavior of the ions has been followed by molecular dynamics with the AMOEBA polarizable force field. Multiply charged ions and small singly charged ions are found to lie inside the droplet, while bigger monovalent ions sit near the surface. The results provide a coherent picture of average structural properties as well as residence times for which a general trend is proposed, especially for the anions.

Clustering of amines and hydrazines in atmospheric nucleation

NASA Astrophysics Data System (ADS)

Li, Siyang; Qu, Kun; Zhao, Hailiang; Ding, Lei; Du, Lin

2016-06-01

It has been proved that the presence of amines in the atmosphere can enhance aerosol formation. Hydrazine (HD) and its substituted derivatives, monomethylhydrazine (MMH) and unsymmetrical dimethylhydrazine (UDMH), which are organic derivatives of amine and ammonia, are common trace atmospheric species that may contribute to the growth of nucleation clusters. The structures of the hydrazine and amine clusters containing one or two common nucleation molecules (ammonia, water, methanol and sulfuric acid) have been optimized using density functional theory (DFT) methods. The clusters growth mechanism has been explored from the thermochemistry by calculating the Gibbs free energies of adding an ammonia, water, methanol or sulfuric acid molecule step by step at room temperature, respectively. The results show that hydrazine and its derivatives could enhance heteromolecular homogeneous nucleation in the earth's atmosphere.

Electronic levels and charge distribution near the interface of nickel

NASA Technical Reports Server (NTRS)

Waber, J. T.

1982-01-01

The energy levels in clusters of nickel atoms were investigated by means of a series of cluster calculations using both the multiple scattering and computational techniques (designated SSO) which avoids the muffin-tin approximation. The point group symmetry of the cluster has significant effect on the energy of levels nominally not occupied. This influences the electron transfer process during chemisorption. The SSO technique permits the approaching atom or molecule plus a small number of nickel atoms to be treated as a cluster. Specifically, molecular levels become more negative in the O atom, as well as in a CO molecule, as the metal atoms are approached. Thus, electron transfer from the nickel and bond formation is facilitated. This result is of importance in understanding chemisorption and catalytic processes.

Stepwise assembly of a semiconducting coordination polymer [Cd8S(SPh)14(DMF)(bpy)]n and its photodegradation of organic dyes.

PubMed

Xu, Chao; Hedin, Niklas; Shi, Hua-Tian; Xin, ZhiFeng; Zhang, Qian-Feng

2015-04-14

Chalcogenolate clusters can be interlinked with organic linkers into semiconducting coordination polymers with photocatalytic properties. Here, discrete clusters of Cd8S(SPh)14(DMF)3 were interlinked with 4,4'-bipyridine into a one dimensional coordination polymer of [Cd8S(SPh)14(DMF)(bpy)]n with helical chains. A stepwise mechanism for the assembly of the coordination polymer in DMF was revealed by an ex situ dynamic light scattering study. The cluster was electrostatically neutral and showed a penta-supertetrahedral structure. During the assembly each cluster was interlinked with two 4,4'-bipyridine molecules, which replaced the two terminal DMF molecules of the clusters. In their solid-state forms, the cluster and the coordination polymer were semiconductors with wide band gaps of 3.08 and 2.80 ev. They photocatalytically degraded rhodamine B and methylene blue in aqueous solutions. The moderate conditions used for the synthesis could allow for further in situ studies of the reaction-assembly of related clusters and coordination polymers.

PREFACE: International Conference on Many Particle Spectroscopy of Atoms, Molecules, Clusters and Surfaces

NASA Astrophysics Data System (ADS)

Dowek, Danielle; Bennani, Azzedine; Lablanquie, Pascal; Maquet, Alfred

2008-12-01

The 2008 edition of the International Conference on Many Particle Spectroscopy of Atoms, Molecules, Clusters and Surfaces was held in Paris from 30 June to 2 July 2008. This biennial conference alternates with the International Symposium on (e,2e), Double Photoionization and Related Topics which is a satellite of the International Conference on Photonic, Electronic and Atomic Collisions (ICPEAC) conference. Over 110 participants from 20 countries gathered to examine the latest developments in the field of radiation interactions with matter. These include electron-electron correlation effects in excitation and in single and multiple ionization of atoms, molecules, clusters and surfaces with various projectiles: electrons, photons and ions. The present proceedings gathers the contributions of invited speakers and is intended to provide a detailed state-of-the-art account of the various facets of the field. Special thanks are due to Université Paris Sud XI, CNRS, and the laboratories LCAM, LIXAM and LCPMR which provided financial support for the organization of the conference. We are also grateful to the contribution of the companies Varian and RoentDek Handels GmbH. Guest Editors: Danielle Dowek and Azzedine Bennani LCAM, Université Paris Sud XI, France Pascal Lablanquie and Alfred Maquet LCPMR, Université Pierre et Marie Curie, Paris, France INTERNATIONAL SCIENTIFIC COMMITTEE Lorenzo Avaldi, (Italy) Alexei Grum Grzhimailo, (Russia) Klaus Bartschat, (USA) Nikolai Kabachnik, (Russia) Jamal Berakdar, (Germany) Birgit Lohmann, (Australia) Nora Berrah, (USA) Don H Madison, (USA) Michael Brunger, (Australia) Francis Penent, (France) Albert Crowe, (UK) Bernard Piraux, (Belgium) Claude Dal Cappello, (France) Roberto Rivarola, (Argentina) JingKang Deng, (China) Emma Sokkel, (Ireland) Alexander Dorn, (Germany) Giovanni Stefani, (Italy) Reinhardt Dorner, (Germany) Noboru Watanabe, (Japan) François Frémont, (France) LOCAL ORGANIZING COMMITTEE Azzedine BENNANI (Chair) - Université Paris-Sud 11, Orsay Danielle DOWEK (co-Chair) - Université Paris-Sud 11, Orsay Bernadette ROME (Secretary) - Université Paris-Sud 11, Orsay Elena Magdalena STAICU CASAGRANDE - Université Paris-Sud 11, Orsay Alain HUETZ - Université Paris-Sud 11, Orsay Laurence MALEGAT - Université Paris-Sud 11, Orsay Michael MEYER - Université Paris-Sud 11, Orsay Adnan NAJA - Université Paris-Sud 11, Orsay Yan PICARD - Université Paris-Sud 11, Orsay Lidija ANDRIC - Université Pierre et Marie Curie, Paris Alain DUBOIS - Université Pierre et Marie Curie, Paris Pascal LABLANQUIE - Université Pierre et Marie Curie, Paris Alfred MAQUET - Université Pierre et Marie Curie, Paris Francis PENENT - Université Pierre et Marie Curie, Paris Patricia SELLES - Université Pierre et Marie Curie, Paris Marc SIMON - Université Pierre et Marie Curie, Paris Conference photograph

Long-Ranged Oppositely Charged Interactions for Designing New Types of Colloidal Clusters

NASA Astrophysics Data System (ADS)

Demirörs, Ahmet Faik; Stiefelhagen, Johan C. P.; Vissers, Teun; Smallenburg, Frank; Dijkstra, Marjolein; Imhof, Arnout; van Blaaderen, Alfons

2015-04-01

Getting control over the valency of colloids is not trivial and has been a long-desired goal for the colloidal domain. Typically, tuning the preferred number of neighbors for colloidal particles requires directional bonding, as in the case of patchy particles, which is difficult to realize experimentally. Here, we demonstrate a general method for creating the colloidal analogs of molecules and other new regular colloidal clusters without using patchiness or complex bonding schemes (e.g., DNA coating) by using a combination of long-ranged attractive and repulsive interactions between oppositely charged particles that also enable regular clusters of particles not all in close contact. We show that, due to the interplay between their attractions and repulsions, oppositely charged particles dispersed in an intermediate dielectric constant (4 <ɛ <10 ) provide a viable approach for the formation of binary colloidal clusters. Tuning the size ratio and interactions of the particles enables control of the type and shape of the resulting regular colloidal clusters. Finally, we present an example of clusters made up of negatively charged large and positively charged small satellite particles, for which the electrostatic properties and interactions can be changed with an electric field. It appears that for sufficiently strong fields the satellite particles can move over the surface of the host particles and polarize the clusters. For even stronger fields, the satellite particles can be completely pulled off, reversing the net charge on the cluster. With computer simulations, we investigate how charged particles distribute on an oppositely charged sphere to minimize their energy and compare the results with the solutions to the well-known Thomson problem. We also use the simulations to explore the dependence of such clusters on Debye screening length κ-1 and the ratio of charges on the particles, showing good agreement with experimental observations.

Electric field-induced reorganization of two-component supported bilayer membranes

PubMed Central

Groves, Jay T.; Boxer, Steven G.; McConnell, Harden M.

1997-01-01

Application of electric fields tangent to the plane of a confined patch of fluid bilayer membrane can create lateral concentration gradients of the lipids. A thermodynamic model of this steady-state behavior is developed for binary systems and tested with experiments in supported lipid bilayers. The model uses Flory’s approximation for the entropy of mixing and allows for effects arising when the components have different molecular areas. In the special case of equal area molecules the concentration gradient reduces to a Fermi–Dirac distribution. The theory is extended to include effects from charged molecules in the membrane. Calculations show that surface charge on the supporting substrate substantially screens electrostatic interactions within the membrane. It also is shown that concentration profiles can be affected by other intermolecular interactions such as clustering. Qualitative agreement with this prediction is provided by comparing phosphatidylserine- and cardiolipin-containing membranes. PMID:9391034

Laser desorption ionization mass spectrometry: Recent progress in matrix-free and label-assisted techniques.

PubMed

Mandal, Arundhoti; Singha, Monisha; Addy, Partha Sarathi; Basak, Amit

2017-10-13

The MALDI-based mass spectrometry, over the last three decades, has become an important analytical tool. It is a gentle ionization technique, usually applicable to detect and characterize analytes with high molecular weights like proteins and other macromolecules. The earlier difficulty of detection of analytes with low molecular weights like small organic molecules and metal ion complexes with this technique arose due to the cluster of peaks in the low molecular weight region generated from the matrix. To detect such molecules and metal ion complexes, a four-prong strategy has been developed. These include use of alternate matrix materials, employment of new surface materials that require no matrix, use of metabolites that directly absorb the laser light, and the laser-absorbing label-assisted LDI-MS (popularly known as LALDI-MS). This review will highlight the developments with all these strategies with a special emphasis on LALDI-MS. © 2017 Wiley Periodicals, Inc.

Electric field-induced reorganization of two-component supported bilayer membranes.

PubMed

Groves, J T; Boxer, S G; McConnell, H M

1997-12-09

Application of electric fields tangent to the plane of a confined patch of fluid bilayer membrane can create lateral concentration gradients of the lipids. A thermodynamic model of this steady-state behavior is developed for binary systems and tested with experiments in supported lipid bilayers. The model uses Flory's approximation for the entropy of mixing and allows for effects arising when the components have different molecular areas. In the special case of equal area molecules the concentration gradient reduces to a Fermi-Dirac distribution. The theory is extended to include effects from charged molecules in the membrane. Calculations show that surface charge on the supporting substrate substantially screens electrostatic interactions within the membrane. It also is shown that concentration profiles can be affected by other intermolecular interactions such as clustering. Qualitative agreement with this prediction is provided by comparing phosphatidylserine- and cardiolipin-containing membranes.

Reaction-diffusion basis of retroviral infectivity

NASA Astrophysics Data System (ADS)

Sadiq, S. Kashif

2016-11-01

Retrovirus particle (virion) infectivity requires diffusion and clustering of multiple transmembrane envelope proteins (Env3) on the virion exterior, yet is triggered by protease-dependent degradation of a partially occluding, membrane-bound Gag polyprotein lattice on the virion interior. The physical mechanism underlying such coupling is unclear and only indirectly accessible via experiment. Modelling stands to provide insight but the required spatio-temporal range far exceeds current accessibility by all-atom or even coarse-grained molecular dynamics simulations. Nor do such approaches account for chemical reactions, while conversely, reaction kinetics approaches handle neither diffusion nor clustering. Here, a recently developed multiscale approach is considered that applies an ultra-coarse-graining scheme to treat entire proteins at near-single particle resolution, but which also couples chemical reactions with diffusion and interactions. A model is developed of Env3 molecules embedded in a truncated Gag lattice composed of membrane-bound matrix proteins linked to capsid subunits, with freely diffusing protease molecules. Simulations suggest that in the presence of Gag but in the absence of lateral lattice-forming interactions, Env3 diffuses comparably to Gag-absent Env3. Initial immobility of Env3 is conferred through lateral caging by matrix trimers vertically coupled to the underlying hexameric capsid layer. Gag cleavage by protease vertically decouples the matrix and capsid layers, induces both matrix and Env3 diffusion, and permits Env3 clustering. Spreading across the entire membrane surface reduces crowding, in turn, enhancing the effect and promoting infectivity. This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

Ro-vibrational Spectra of (para-H2 )N -CH4 in He Droplets.

PubMed

Hoshina, Hiromichi; Sliter, Russell; Ravi, Aakash; Kuma, Susumu; Momose, Takamasa; Vilesov, Andrey F

2016-11-18

In this work, we report on the infrared spectroscopic study of clusters of CH 4 molecules with up to N=80 para-hydrogen molecules assembled inside He droplets. Upon increase of the number of the added para-hydrogen molecules up to about N=12, both the rotational constant, B, and the origin frequency of the υ 3 band of CH 4 decrease gradually. In the range of 6 ≤N≤12, the spectra indicate some abrupt changes of B and υ 3 with both values being approximately constant at N≥12. The origin of this effect is discussed. Comparison of the spectra of methane molecules in para-hydrogen clusters to that in solid para-hydrogen is also presented. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Exploring Connectivity in Sequence Space of Functional RNA

NASA Technical Reports Server (NTRS)

Wei, Chenyu; Pohorille, Andrzej; Popovic, Milena; Ditzler, Mark

2017-01-01

Emergence of replicable genetic molecules was one of the marking points in the origin of life, evolution of which can be conceptualized as a walk through the space of all possible sequences. A theoretical concept of fitness landscape helps to understand evolutionary processes through assigning a value of fitness to each genotype. Then, evolution of a phenotype is viewed as a series of consecutive, single-point mutations. Natural selection biases evolution toward peaks of high fitness and away from valleys of low fitness. whereas neutral drift occurs in the sequence space without direction as mutations are introduced at random. Large networks of neutral or near-neutral mutations on a fitness landscape, especially for sufficiently long genomes, are possible or even inevitable. Their detection in experiments, however, has been elusive. Although a few near-neutral evolutionary pathways have been found, recent experimental evidence indicates landscapes consist of largely isolated islands. The generality of these results, however, is not clear, as the genome length or the fraction of functional molecules in the genotypic space might have been insufficient for the emergence of large, neutral networks. Thorough investigation on the structure of the fitness landscape is essential to understand the mechanisms of evolution of early genomes. RNA molecules are commonly assumed to play the pivotal role in the origin of genetic systems. They are widely believed to be early, if not the earliest, genetic and catalytic molecules, with abundant biochemical activities as aptamers and ribozymes, i.e. RNA molecules capable, respectively, to bind small molecules or catalyze chemical reactions. Here, we present results of our recent studies on the structure of the sequence space of RNA ligase ribozymes selected through in vitro evolution. Several hundred thousands of sequences active to a different degree were obtained by way of deep sequencing. Analysis of these sequences revealed several large clusters defined such that every sequence in a cluster can be reached from any other sequence in the same cluster through a series of single point mutations. Sequences in a single cluster appear to adopt more than one secondary structure. The mechanism of refolding within a single cluster was examined. To shed light on possible evolutionary paths in the space of ribozymes, the connectivity between clusters was investigated. The effect of length of RNA molecules on the structure of the fitness landscape and possible evolutionary paths was examined by way of comparing functional sequences of 20 and 80 nucleobases in length. It was found that sequences of different lengths shared secondary structure motifs that were presumed responsible for catalytic activity, with increasing complexity and global structural rearrangements emerging in longer molecules.

Electronic spectroscopy and photodissociation dynamics of Co(2+)-methanol clusters: Co2+ (CH3OH)n (n = 4-7).

PubMed

Thompson, Christopher J; Faherty, Kieron P; Stringer, Kay L; Metz, Ricardo B

2005-03-07

Solvated cluster ions Co2+ (CH3OH)n (n = 4-7) have been produced by electrospray and studied using photofragment spectroscopy. There are notable differences between the photodissociation spectra of these complexes and the analogous water complexes. Co2+ (CH3OH)6 absorbs significantly more strongly than Co2+ (H2O)6. The photodissociation spectra of Co2+ (CH3OH)n (n = 4, 5 and 6) are very similar, which suggests that they share the Co2+ (CH3OH)4 chromophore, with additional solvent molecules in the second shell. In contrast, our earlier studies indicate that Co2+ (H2O)6 is six coordinate, and its spectrum is significantly different from that of Co2+ (H2O)4. The larger clusters Co2+ (CH3OH)n (n = 5-7) dissociate by simple loss of one or more solvent molecules. Larger clusters tend to lose more solvent molecules, especially at higher photon energies. As with the corresponding water cluster, Co2+ (CH3OH)4 photodissociates by proton transfer through a salt-bridge intermediate. This is accompanied by a modest kinetic energy release of 170 kJ mol(-1) and occurs with a lifetime of 145 ns.

Spectroscopic study of active phase-support interactions on a RhO{sub x}/CeO{sub 2} catalyst: Evidence for electronic interactions

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

Martinez-Arias, A.; Soria, J.; Conesa, J.C.

The effects of thermal treatments under vacuum, used as a way to generate reduced centers on Rh{sub 2}O{sub 3} and RhO{sub x}/CeO{sub 2}, have been studied by ESR and FTIR, using respectively oxygen and carbon monoxide as probe molecules. The results obtained for the outgassed samples reveal the presence of ceria-rhodia interactions favoring the stabilization of paramagnetic Rh{sup 2+} cations in rhodium oxide clusters on the ceria surface. Subsequent O{sub 2} adsorption leads to the formation of different oxygen-related paramagnetic species located on ceria, on rhodium oxide clusters and at the boundary between both oxides; their contribution to the spectramore » depends on outgassing conditions and O{sub 2} adsorption temperature. The unexpected absence of O{sub 2}{sup -}-Ce{sup 4+} species after O{sub 2} contact at 77 K with RhO{sub x}/CeO{sub 2} outgassed above 573 K evidences the existence of electronic interactions between the RhO{sub x}, and CeO{sub 2} phases, being explained on the basis of electron transfer to the mixed valence RhO{sub x}, phase from the surface-reduced ceria, leading to electron depletion of the latter. This effect is inhibited by CO adsorption, showing the dependence between the electron-accepting properties of the rhodia clusters and the presence of vacant coordination sites at the surface Rh ions. An effect of similar kind may be responsible for shifts observed in the IR bands of rhodium dicarbonyls formed in the RhO{sub x}/CeO{sub 2} system. The latter results suggest the possibility that thermal enhancement of surface reactions in complex systems could depend on electron transfer between adjacent phases and that adsorption on one phase may influence the surface reactivity of another phase by affecting to the electron transfer between them. 34 refs., 8 figs., 2 tabs.« less

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

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

Hu, Lin; Maroudas, Dimitrios, E-mail: maroudas@ecs.umass.edu; Hammond, Karl D.

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 ofmore » 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.« less

New ab initio adiabatic potential energy surfaces and bound state calculations for the singlet ground X˜ 1A1 and excited C˜ 1B2(21A') states of SO2

NASA Astrophysics Data System (ADS)

Kłos, Jacek; Alexander, Millard H.; Kumar, Praveen; Poirier, Bill; Jiang, Bin; Guo, Hua

2016-05-01

We report new and more accurate adiabatic potential energy surfaces (PESs) for the ground X˜ 1A1 and electronically excited C˜ 1B2(21A') states of the SO2 molecule. Ab initio points are calculated using the explicitly correlated internally contracted multi-reference configuration interaction (icMRCI-F12) method. A second less accurate PES for the ground X ˜ state is also calculated using an explicitly correlated single-reference coupled-cluster method with single, double, and non-iterative triple excitations [CCSD(T)-F12]. With these new three-dimensional PESs, we determine energies of the vibrational bound states and compare these values to existing literature data and experiment.

On Ion Clusters in the Interstellar Gas

NASA Technical Reports Server (NTRS)

Donn, Bertram

1960-01-01

In a recent paper V.I. Krassovsky (1958) predicts the occurrence of clusters of large numbers of atoms and molecules around ions in the interstellar gas. He then proposes a number of physicochemical processes that would be considerably enhanced by the high particle density in such clusters. In particular, he suggests that absorption by negative ions formed in the clusters would account for the interstellar extinction without any necessity for the presence of grains. Because of the important consequences that ion clusters could have, it is necessary to examine their occurrence more fully. This note re-examines the formation of ion clusters in space and shows that even ion-molecule pairs are essentially non-existent. Ion clusters have been considered by Bloom and Margenau (1952) from the same point of view as that used by Krassovsky, whose basic reference (Joffe and Semenov 1933) unfortunately is not available. A different approach has been used by Eyring, Hirschfelder, and Taylor (1936) following the methods of chemical equilibrium. Both the references cited here enable one to conclude that clustering is negligible. Therefore, the treatment of Eyring et al. is more appropriate than the method of Bloom and Margenau, which depends on the statistical equilibrium of an atmosphere in a force field.

Role of clusters in nonclassical nucleation and growth of protein crystals

PubMed Central

Sleutel, Mike; Van Driessche, Alexander E. S.

2014-01-01

The development of multistep nucleation theory has spurred on experimentalists to find intermediate metastable states that are relevant to the solidification pathway of the molecule under interest. A great deal of studies focused on characterizing the so-called “precritical clusters” that may arise in the precipitation process. However, in macromolecular systems, the role that these clusters might play in the nucleation process and in the second stage of the precipitation process, i.e., growth, remains to a great extent unknown. Therefore, using biological macromolecules as a model system, we have studied the mesoscopic intermediate, the solid end state, and the relationship that exists between them. We present experimental evidence that these clusters are liquid-like and stable with respect to the parent liquid and metastable compared with the emerging crystalline phase. The presence of these clusters in the bulk liquid is associated with a nonclassical mechanism of crystal growth and can trigger a self-purifying cascade of impurity-poisoned crystal surfaces. These observations demonstrate that there exists a nontrivial connection between the growth of the macroscopic crystalline phase and the mesoscopic intermediate which should not be ignored. On the other hand, our experimental data also show that clusters existing in protein solutions can significantly increase the nucleation rate and therefore play a relevant role in the nucleation process. PMID:24449867

The role of highly oxygenated molecules (HOMs) in determining the composition of ambient ions in the boreal forest

NASA Astrophysics Data System (ADS)

Bianchi, Federico; Garmash, Olga; He, Xucheng; Yan, Chao; Iyer, Siddharth; Rosendahl, Ida; Xu, Zhengning; Rissanen, Matti P.; Riva, Matthieu; Taipale, Risto; Sarnela, Nina; Petäjä, Tuukka; Worsnop, Douglas R.; Kulmala, Markku; Ehn, Mikael; Junninen, Heikki

2017-11-01

In order to investigate the negative ions in the boreal forest we have performed measurements to chemically characterise the composition of negatively charged clusters containing highly oxygenated molecules (HOMs). Additionally, we compared this information with the chemical composition of the neutral gas-phase molecules detected in the ambient atmosphere during the same period. The chemical composition of the ions was retrieved using an atmospheric pressure interface time-of-flight mass spectrometer (APi-TOF-MS) while the gas-phase neutral molecules (mainly sulfuric acid and HOMs) were characterised using the same mass spectrometer coupled to a nitrate-based chemical ionisation unit (CI-APi-TOF). Overall, we divided the identified HOMs in two classes: HOMs containing only carbon, hydrogen and oxygen and nitrogen-containing HOMs or organonitrates (ONs). During the day, among the ions, in addition to the well-known pure sulfuric acid clusters, we found a large number of HOMs clustered with nitrate (NO3-) or bisulfate (HSO4-), with the first one being more abundant. During the night, the distribution of ions, mainly composed of HOM clustered with NO3-, was very similar to the neutral compounds that are detected in the CI-APi-TOF as adducts with the artificially introduced primary ion (NO3-). For the first time, we identified several clusters containing up to 40 carbon atoms. These ions are formed by up to four oxidised α-pinene units clustered with NO3-. While we know that dimers (16-20 carbon atoms) are probably formed by a covalent bond between two α-pinene oxidised units, it is still unclear what bonding formed larger clusters. Finally, diurnal profiles of the negative ions were consistent with the neutral compounds revealing that ONs peak during the day while HOMs are more abundant at night-time. However, during the day, a large fraction of the negative charge is taken up by the pure sulfuric acid clusters causing differences between ambient ions and neutral compounds (i.e. less available charge for HOM and ON).

Tailored Rh surface facilitates, enhancement of Raman scattering in trimetallic AuPt core/Rh shell composites: Experimental and theoretical evidences

NASA Astrophysics Data System (ADS)

Loganathan, B.; Chandraboss, V. L.; Senthilvelan, S.; Karthikeyan, B.

2016-01-01

We present a detailed analysis of surface-enhanced Raman scattering of 7-azaindole and L-cysteine adsorbed on a tailored Rh surface by using experimental and density functional theoretical (DFT) calculations. DFT with the B3LYP/Lanl2DZ basis set was used for the optimization of the ground state geometries and simulation of the surface-enhanced Raman spectrum of probe molecules adsorbed on Rh6 cluster. 7-azaindole and L-cysteine adsorption at the shell interface was ascertained from first-principles. In addition, characterization of synthesized trimetallic AuPt core/Rh shell colloidal nanocomposites has been analyzed by UV-visible spectroscopy, high-resolution transmission and scanning electron microscopy, selected area electron diffraction pattern analysis, energy-dispersive X-ray spectroscopy, atomic force, confocal Raman microscopy, FT-Raman and surface-enhanced Raman spectroscopic analysis. This analysis serves as the first step in gaining an accurate understanding of specific interactions at the interface of organic and biomolecules and to gain knowledge on the surface composition of trimetallic Au/Pt/Rh colloidal nanocomposites.

Analysis of heterogeneous water vapor uptake by metal iodide cluster ions via differential mobility analysis-mass spectrometry

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

Oberreit, Derek; Fluid Measurement Technologies, Inc., Saint Paul, Minnesota 55110; Rawat, Vivek K.

The sorption of vapor molecules onto pre-existing nanometer sized clusters is of importance in understanding particle formation and growth in gas phase environments and devising gas phase separation schemes. Here, we apply a differential mobility analyzer-mass spectrometer based approach to observe directly the sorption of vapor molecules onto iodide cluster ions of the form (MI){sub x}M{sup +} (x = 1-13, M = Na, K, Rb, or Cs) in air at 300 K and with water saturation ratios in the 0.01-0.64 range. The extent of vapor sorption is quantified in measurements by the shift in collision cross section (CCS) for eachmore » ion. We find that CCS measurements are sensitive enough to detect the transient binding of several vapor molecules to clusters, which shift CCSs by only several percent. At the same time, for the highest saturation ratios examined, we observed CCS shifts of up to 45%. For x < 4, cesium, rubidium, and potassium iodide cluster ions are found to uptake water to a similar extent, while sodium iodide clusters uptake less water. For x ≥ 4, sodium iodide cluster ions uptake proportionally more water vapor than rubidium and potassium iodide cluster ions, while cesium iodide ions exhibit less uptake. Measured CCS shifts are compared to predictions based upon a Kelvin-Thomson-Raoult (KTR) model as well as a Langmuir adsorption model. We find that the Langmuir adsorption model can be fit well to measurements. Meanwhile, KTR predictions deviate from measurements, which suggests that the earliest stages of vapor uptake by nanometer scale species are not well described by the KTR model.« less

Chemistry Within Molecular Clusters

DTIC Science & Technology

1992-06-01

reactions, and only occur within van der Waals clusters. 23 They include the generation of (C2H4F2),>4H+ ions from 1,1- difluoroethane clusters, 4 the...of fragment ions, and identification of the molecule must be made by the characteristic fragmentation pattern. The mass spectrum of 1,1- difluoroethane

Chemistry within Molecular Clusters

DTIC Science & Technology

1992-05-29

within van der Waals clusters. 23 They include the generation of (C2H4F 2),,>4H+ ions from 1,1- difluoroethane clusters, 24 the generation of (CH 3...fragment ions, and identification of the molecule must be made by the characteristic fragmentation pattern. The mass spectrum of 1,1- difluoroethane (DFE

The Heat of Formation of HNO

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Dateo, Christopher E.

1995-01-01

The HNO molecule is of interest in both combustion and atmospheric chemistry. For example, Guadagnini et al. have recently presented ab initio potential energy surfaces for the three lowest lying electronic states of HNO and then used these in examining several chemical reactions that take place in the combustion of nitrogen containing fuels and in the oxidation of atmospheric nitrogen. We have previously studied the ground state potential energy surface (i.e., stationary points along the HNO reversible reaction HON path), vibrational spectrum (using an accurate quartic force field), zero-point energy, and bonding of HNO using coupled-cluster ab initio methods. HNO is also very interesting because of the unique nature of its bonding characteristics. That is, the potential energy surface is very flat along the H-N bonding coordinate thereby giving unusual harmonic and fundamental vibrational frequencies, and the H-N bond energy is rather weak in comparison to other H-N bond energies. In fact, using experimental heats of formation for HNO, H, and NO, the H- bond energy is computed to be only 49.9 kcal/ mol (298 K). However, ab initio calculations of isodesmic reaction energies involving HNO, FNO, ClNO, and several other molecules have shown that there is an inconsistency in the experimental heats of formation of the XNO (X double bond H, F, and Cl) species. Hence the motivation for this study was to determine a very accurate (Delta)H(sub f, sup o) value for HNO using state-of-the-art ab initio methods. Based on many recent studies it is evident that the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, denoted CCSD(T), in conjunction with large one-particle basis sets should be reliable to better than +/- 0.8 kcal/mol for this quantity. The computational methodology is described in the next section followed by our results and discussion. Conclusions are presented in the final section.

The Heat of Formation of HNO

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Dateo, Christopher E.

1995-01-01

The HNO molecule is of interest in both combustion and atmospheric chemistry. For example, Guadagnini et al. have recently presented ab initio potential energy surfaces for the three lowest lying electronic states of HNO and then used these in examining several chemical reactions that take place in the combustion of nitrogen containing fuels and in the oxidation of atmospheric nitrogen. We have previously studied the ground state potential energy surface (i.e., stationary points along the HNO rev. reaction HON path), vibrational spectrum (using an accurate quartic force field), zero-point energy, and bonding of HNO using coupled-cluster ab initio methods. HNO is also very interesting because of the unique nature of its bonding characteristics. That is, the potential energy surface is very flat along the H-N bonding coordinate thereby giving unusual harmonic and fundamental vibrational frequencies, and the H-N bond energy is rather weak in comparison to other H-N bond energies. In fact, using experimental heats of formation for HO, H, and NO, the H- bond energy is computed to be only 49.9 kcal/ mol (298 K). However, ab initio calculations of isodesmic reaction energies involving HNO, FNO, ClNO, and several other molecules have shown that there is an inconsistency in the experimental heats of formation of the XNO (X=H, F, and Cl) species. Hence the motivation for this study was to determine a very accurate(DELTA)H(sup o)(sub f) value for HNO using state of-the-art ab initio methods. Based on many recent studies it is evident that the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, denoted CCSD(T), in conjunction with large one-particle basis sets should be reliable to better than +0.8 kcal/mol for this quantity. The computational methodology is described in the next section followed by our results and discussion. Conclusions are presented in the final section.

Large heat capacity change in a protein-monovalent cation interaction.

PubMed

Guinto, E R; Di Cera, E

1996-07-09

Current views about protein-ligand interactions state that electrostatic forces drive the binding of charged species and that burial of hydrophobic and polar surfaces controls the heat capacity change associated with the reaction. For the interaction of a protein with a monovalent cation the electrostatic components are expected to be significant due to the ionic nature of the ligand, whereas the heat capacity change is expected to be small due to the size of the surface area involved in the recognition event. The physiologically important interaction of Na+ with thrombin was studied over the temperature range from 5 to 45 degrees C and the ionic strength range from 50 to 800 mM. These measurements reveal an unanticipated result that bears quite generally on studies of molecular recognition and protein folding. Binding of Na+ to thrombin is characterized by a modest dependence on ionic strength but a large and negative heat capacity change of -1.1 +/- 0.1 kcal mol-1 K-1. The small electrostatic coupling can be explained in terms of a minimal perturbation of the ionic atmosphere of the protein upon Na+ binding. The large heat capacity change, however, is difficult to reconcile with current views on the origin of this effect from surface area changes or large folding transitions coupled to binding. It is proposed that this change is linked to burial of a large cluster of water molecules in the Na+ binding pocket upon Na+ binding. Due to their reduced mobility and highly ordered structure, water molecules sequestered in the interior of a protein must have a lower heat capacity compared to those on the surface of a protein or in the bulk solvent. Hence, a binding or folding event where water molecules are buried may result in significant heat capacity changes independent of changes in exposed hydrophobic surface or coupled conformational transitions.

Low energy isomers of (H{sub 2}O){sub 25} from a hierarchical method based on Monte Carlo temperature basin paving and molecular tailoring approaches benchmarked by MP2 calculations

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

Sahu, Nityananda; Gadre, Shridhar R., E-mail: gadre@iitk.ac.in, E-mail: sotiris.xantheas@pnnl.gov; Rakshit, Avijit

2014-10-28

We report new global minimum candidate structures for the (H{sub 2}O){sub 25} cluster that are lower in energy than the ones reported previously and correspond to hydrogen bonded networks with 42 hydrogen bonds and an interior, fully coordinated water molecule. These were obtained as a result of a hierarchical approach based on initial Monte Carlo Temperature Basin Paving sampling of the cluster's Potential Energy Surface with the Effective Fragment Potential, subsequent geometry optimization using the Molecular Tailoring Approach with the fragments treated at the second order Møller-Plesset (MP2) perturbation (MTA-MP2) and final refinement of the entire cluster at the MP2more » level of theory. The MTA-MP2 optimized cluster geometries, constructed from the fragments, were found to be within <0.5 kcal/mol from the minimum geometries obtained from the MP2 optimization of the entire (H{sub 2}O){sub 25} cluster. In addition, the grafting of the MTA-MP2 energies yields electronic energies that are within <0.3 kcal/mol from the MP2 energies of the entire cluster while preserving their energy rank order. Finally, the MTA-MP2 approach was found to reproduce the MP2 harmonic vibrational frequencies, constructed from the fragments, quite accurately when compared to the MP2 ones of the entire cluster in both the HOH bending and the OH stretching regions of the spectra.« less

Electronic structure and surface properties of MgB2(0001) upon oxygen adsorption

NASA Astrophysics Data System (ADS)

Kim, Chang-Eun; Ray, Keith G.; Bahr, David F.; Lordi, Vincenzo

2018-05-01

We use density-functional theory to investigate the bulk and surface properties of MgB2. The unique bonding structure of MgB2 is investigated by Bader's atoms-in-molecules, charge density difference, and occupancy projected band structure analyses. Oxygen adsorption on the charge-depleted surfaces of MgB2 is studied by a surface potential energy mapping method, reporting a complete map including low-symmetry binding sites. The B-terminated MgB2(0001) demonstrates reconstruction of the graphenelike B layer, and the reconstructed geometry exposes a threefold site of the subsurface Mg, making it accessible from the surface. Detailed reconstruction mechanisms are studied by simulated annealing method based on ab initio molecular dynamics and nudged elastic band calculations. The surface clustering of B atoms significantly modifies the B 2 p states to occupy low energy valence states. The present paper emphasizes that a thorough understanding of the surface phase may explain an apparent inconsistency in the experimental surface characterization of MgB2. Furthermore, these results suggest that the surface passivation can be an important technical challenge when it comes to development of a superconducting device using MgB2.

Novel INTeraction of MUC4 and galectin: potential pathobiological implications for metastasis in lethal pancreatic cancer.

PubMed

Senapati, Shantibhusan; Chaturvedi, Pallavi; Chaney, William G; Chakraborty, Subhankar; Gnanapragassam, Vinayaga S; Sasson, Aaron R; Batra, Surinder K

2011-01-15

Several studies have reported aberrant expression of MUC4 in pancreatic cancer (PC), which is associated with tumorigenicity and metastasis. Mechanisms through which MUC4 promote metastasis of PC cells to distant organs are poorly defined. Identification of MUC4-galectin-3 interaction and its effect on the adhesion of cancer cells to endothelial cells were done by immunoprecipitation and cell-cell adhesion assays, respectively. Serum galectin-3 level for normal and PC patients were evaluated through ELISA. In the present study, we have provided clinical evidence that the level of galectin-3 is significantly elevated in the sera of PC patients with metastatic disease compared with patients without metastasis (P = 0.04) and healthy controls (P = 0.00001). Importantly, for the first time, we demonstrate that MUC4 present on the surface of circulating PC cells plays a significant role in the transient and reversible attachment (docking) of circulating tumor cells to the surface of endothelial cells. Further, exogenous galectin-3 at concentrations similar to that found in the sera of PC patients interacts with MUC4 via surface glycans such as T antigens, which results in the clustering of MUC4 on the cell surface and a stronger attachment (locking) of circulating tumor cells to the endothelium. Altogether, these findings suggest that PC cell-associated MUC4 helps in the docking of tumor cells on the endothelial surface. During cancer progression, MUC4-galectin-3 interaction-mediated clustering of MUC4 may expose the surface adhesion molecules, which in turn promotes a stronger attachment (locking) of tumor cells to the endothelial surface. ©2010 AACR.

Force-activatable coating enables high-resolution cellular force imaging directly on regular cell culture surfaces.

PubMed

Sarkar, Anwesha; Zhao, Yuanchang; Wang, Yongliang; Wang, Xuefeng

2018-06-25

Integrin-transmitted cellular forces are crucial mechanical signals regulating a vast range of cell functions. Although various methods have been developed to visualize and quantify cellular forces at the cell-matrix interface, a method with high performance and low technical barrier is still in demand. Here we developed a force-activatable coating (FAC), which can be simply coated on regular cell culture apparatus' surfaces by physical adsorption, and turn these surfaces to force reporting platforms that enable cellular force mapping directly by fluorescence imaging. The FAC molecule consists of an adhesive domain for surface coating and a force-reporting domain which can be activated to fluoresce by integrin molecular tension. The tension threshold required for FAC activation is tunable in 10-60 piconewton (pN), allowing the selective imaging of cellular force contributed by integrin tension at different force levels. We tested the performance of two FACs with tension thresholds of 12 and 54 pN (nominal values), respectively, on both glass and polystyrene surfaces. Cellular forces were successfully mapped by fluorescence imaging on all the surfaces. FAC-coated surfaces also enable co-imaging of cellular forces and cell structures in both live cells and immunostained cells, therefore opening a new avenue for the study of the interplay of force and structure. We demonstrated the co-imaging of integrin tension and talin clustering in live cells, and concluded that talin clustering always occurs before the generation of integrin tension above 54 pN, reinforcing the notion that talin is an important adaptor protein for integrin tension transmission. Overall, FAC provides a highly convenient approach that is accessible to general biological laboratories for the study of cellular forces with high sensitivity and resolution, thus holding the potential to greatly boost the research of cell mechanobiology.

Polymorphism of Lysozyme Condensates.

PubMed

Safari, Mohammad S; Byington, Michael C; Conrad, Jacinta C; Vekilov, Peter G

2017-10-05

Protein condensates play essential roles in physiological processes and pathological conditions. Recently discovered mesoscopic protein-rich clusters may act as crucial precursors for the nucleation of ordered protein solids, such as crystals, sickle hemoglobin polymers, and amyloid fibrils. These clusters challenge settled paradigms of protein condensation as the constituent protein molecules present features characteristic of both partially misfolded and native proteins. Here we employ the antimicrobial enzyme lysozyme and examine the similarities between mesoscopic clusters, amyloid structures, and disordered aggregates consisting of chemically modified protein. We show that the mesoscopic clusters are distinct from the other two classes of aggregates. Whereas cluster formation and amyloid oligomerization are both reversible, aggregation triggered by reduction of the intramolecular S-S bonds is permanent. In contrast to the amyloid structures, protein molecules in the clusters retain their enzymatic activity. Furthermore, an essential feature of the mesoscopic clusters is their constant radius of less than 50 nm. The amyloid and disordered aggregates are significantly larger and rapidly grow. These findings demonstrate that the clusters are a product of limited protein structural flexibility. In view of the role of the clusters in the nucleation of ordered protein solids, our results suggest that fine-tuning the degree of protein conformational stability is a powerful tool to control and direct the pathways of protein condensation.

Electron-induced chemistry in imidazole clusters embedded in helium nanodroplets

NASA Astrophysics Data System (ADS)

Kuhn, Martin; Raggl, Stefan; Martini, Paul; Gitzl, Norbert; Darian, Masoomeh Mahmoodi; Goulart, Marcelo; Postler, Johannes; Feketeová, Linda; Scheier, Paul

2018-02-01

Electron-induced chemistry in imidazole (IMI) clusters embedded in helium nanodroplets (with an average size of 2 × 105 He atoms) has been investigated with high-resolution time-of-flight mass spectrometry. The formation of both, negative and positive, ions was monitored as a function of the cluster size n. In both ion spectra a clear series of peaks with IMI cluster sizes up to at least 25 are observed. While the anions are formed by collisions of IMI n with He*-, the cations are formed through ionization of IMI n by He+ as the measured onset for the cation formation is observed at 24.6 eV (ionization energy of He). The most abundant series of anions are dehydrogenated anions IMI n-1(IMI-H)-, while other anion series are IMI clusters involving CN and C2H4 moieties. The formation of cations is dominated by the protonated cluster ions IMI n H+, while the intensity of parent cluster cations IMI n + is also observed preferentially for the small cluster size n. The observation of series of cluster cations [IMI n CH3]+ suggests either CH3+ cation to be solvated by n neutral IMI molecules, or the electron-induced chemistry has led to the formation of protonated methyl-imidazole solvated by ( n - 1) neutral IMI molecules.

Creating Quasi Two-Dimensional Cluster-Assembled Materials through Self-Assembly of a Janus Polyoxometalate-Silsesquioxane Co-Cluster.

PubMed

Wu, Han; Zhang, Yu-Qi; Hu, Min-Biao; Ren, Li-Jun; Lin, Yue; Wang, Wei

2017-05-30

Clusters are an important class of nanoscale molecules or superatoms that exhibit an amazing diversity in structure, chemical composition, shape, and functionality. Assembling two types of clusters is creating emerging cluster-assembled materials (CAMs). In this paper, we report an effective approach to produce quasi two-dimensional (2D) CAMs of two types of spherelike clusters, polyhedral oligomeric silsesquioxanes (POSS), and polyoxometalates (POM). To avoid macrophase separation between the two clusters, they are covalently linked to form a POM-POSS cocluster with Janus characteristics and a dumbbell shape. This Janus characteristics enables the cocluster to self-assemble into diverse nanoaggregates, as conventional amphiphilic molecules and macromolecules do, in selective solvents. In our study, we obtained micelles, vesicles, nanosheets, and nanoribbons by tuning the n-hexane content in mixed solvents of acetone and n-hexane. Ordered packing of clusters in the nanosheets and nanoribbons were directly visualized using high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) technique. We infer that the increase of packing order results in the vesicle-to-sheet transition and the change in packing mode causes the sheet-to-ribbon transitions. Our findings have verified the effectivity of creating quasi 2D cluster-assembled materials though the cocluster self-assembly as a new approach to produce novel CAMs.

Snapshots of crystal growth: Nanoclusters of organic conductors on Au(111) surfaces

NASA Astrophysics Data System (ADS)

Schott, J. H.; Ward, M. D.

1994-06-01

Mono- and multilayer crystalline nanoclusters of tetra-hiafulvalene-tetracyanoquinodimethane ((TTF) (TCNO)), a low-dimensional organic conductor in the bulk form, can be formed readily on Au(111) surfaces by vapor phase sublimation under ambient conditions. Scanning tunneling microscopy of monolayer (TTF)(TCNQ) films reveals a two-dimensional density of states (DOS) that is consistent with the arrangement of TTF and TCNO molecules in the ac face of bulk (TTF)(TCNO), in which the molecular planes are nearly parallel to the Au(111) substrate. In contrast, clusters with thicknesses corresponding to two or three molecular layers exhibit a transformation to a highly anisotropic DOS that can be attributed to interlayer molecular overlap in segregated TTF and TCNQ molecular chains along the c-axis, which can be described as 'molecular wires'. The orientation of the crystalline (TTF)(TCNO) clusters is preserved throughout the crystal growth sequence, leading to meso- and macroscopic (TTF)(TCNO) needles that are oriented perpendicular to the Au(111) substrate. These studies provide visualization of crystal growth from the initial stages of nucleation to macroscopic crystals, and a revealing example of the changes in electronic structure that occur during the evolution of molecular (TTF)(TCNQ) nuclei into a bulk crystalline phase.

Quantum dynamics of small H2 and D2 clusters in the large cage of structure II clathrate hydrate: Energetics, occupancy, and vibrationally averaged cluster structures

NASA Astrophysics Data System (ADS)

Sebastianelli, Francesco; Xu, Minzhong; Bačić, Zlatko

2008-12-01

We report diffusion Monte Carlo (DMC) calculations of the quantum translation-rotation (T-R) dynamics of one to five para-H2 (p-H2) and ortho-D2 (o-D2) molecules inside the large hexakaidecahedral (51264) cage of the structure II clathrate hydrate, which was taken to be rigid. These calculations provide a quantitative description of the size evolution of the ground-state properties, energetics, and the vibrationally averaged geometries, of small (p-H2)n and (o-D2)n clusters, n=1-5, in nanoconfinement. The zero-point energy (ZPE) of the T-R motions rises steeply with the cluster size, reaching 74% of the potential well depth for the caged (p-H2)4. At low temperatures, the rapid increase of the cluster ZPE as a function of n is the main factor that limits the occupancy of the large cage to at most four H2 or D2 molecules, in agreement with experiments. Our DMC results concerning the vibrationally averaged spatial distribution of four D2 molecules, their mean distance from the cage center, the D2-D2 separation, and the specific orientation and localization of the tetrahedral (D2)4 cluster relative to the framework of the large cage, agree very well with the low-temperature neutron diffraction experiments involving the large cage with the quadruple D2 occupancy.

Quantum dynamics of small H2 and D2 clusters in the large cage of structure II clathrate hydrate: energetics, occupancy, and vibrationally averaged cluster structures.

PubMed

Sebastianelli, Francesco; Xu, Minzhong; Bacić, Zlatko

2008-12-28

We report diffusion Monte Carlo (DMC) calculations of the quantum translation-rotation (T-R) dynamics of one to five para-H(2) (p-H(2)) and ortho-D(2) (o-D(2)) molecules inside the large hexakaidecahedral (5(12)6(4)) cage of the structure II clathrate hydrate, which was taken to be rigid. These calculations provide a quantitative description of the size evolution of the ground-state properties, energetics, and the vibrationally averaged geometries, of small (p-H(2))(n) and (o-D(2))(n) clusters, n=1-5, in nanoconfinement. The zero-point energy (ZPE) of the T-R motions rises steeply with the cluster size, reaching 74% of the potential well depth for the caged (p-H(2))(4). At low temperatures, the rapid increase of the cluster ZPE as a function of n is the main factor that limits the occupancy of the large cage to at most four H(2) or D(2) molecules, in agreement with experiments. Our DMC results concerning the vibrationally averaged spatial distribution of four D(2) molecules, their mean distance from the cage center, the D(2)-D(2) separation, and the specific orientation and localization of the tetrahedral (D(2))(4) cluster relative to the framework of the large cage, agree very well with the low-temperature neutron diffraction experiments involving the large cage with the quadruple D(2) occupancy.

Uniform deposition of size-selected clusters using Lissajous scanning

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

Beniya, Atsushi; Watanabe, Yoshihide, E-mail: e0827@mosk.tytlabs.co.jp; Hirata, Hirohito

2016-05-15

Size-selected clusters can be deposited on the surface using size-selected cluster ion beams. However, because of the cross-sectional intensity distribution of the ion beam, it is difficult to define the coverage of the deposited clusters. The aggregation probability of the cluster depends on coverage, whereas cluster size on the surface depends on the position, despite the size-selected clusters are deposited. It is crucial, therefore, to deposit clusters uniformly on the surface. In this study, size-selected clusters were deposited uniformly on surfaces by scanning the cluster ions in the form of Lissajous pattern. Two sets of deflector electrodes set in orthogonalmore » directions were placed in front of the sample surface. Triangular waves were applied to the electrodes with an irrational frequency ratio to ensure that the ion trajectory filled the sample surface. The advantages of this method are simplicity and low cost of setup compared with raster scanning method. The authors further investigated CO adsorption on size-selected Pt{sub n} (n = 7, 15, 20) clusters uniformly deposited on the Al{sub 2}O{sub 3}/NiAl(110) surface and demonstrated the importance of uniform deposition.« less

Molecular Dynamics Studies of Thermal Induced Chemistry in Tatb

NASA Astrophysics Data System (ADS)

Quenneville, J.; Germann, T. C.; Thompson, A. P.; Kober, E. M.

2007-12-01

A reactive force field (ReaxFF) is used with molecular dynamics to probe the chemistry induced by intense heating (`accelerated cook-off') of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). Large-system simulations are desired for TATB because of the high degree of carbon clustering expected in this material. Using small, 32-molecule simulations, we calculate the reaction rate as a function of temperature and compare the Arrhenius-predicted activation energy with experiment. Decomposition product evolution (mainly N2, H2O, CO2 and graphitic carbon clusters) is followed using a 576-molecule larger simulation, which also illustrates the effect of system size on both carbon clustering and reaction rate.

Giant Spherical Cluster with I-C140 Fullerene Topology.

PubMed

Heinl, Sebastian; Peresypkina, Eugenia; Sutter, Jörg; Scheer, Manfred

2015-11-02

We report on an effective cluster expansion of CuBr-linked aggregates by the increase of the steric bulk of the Cp(R) ligand in the pentatopic molecules [Cp(R)Fe(η(5)-P5)]. Using [Cp(BIG)Fe(η(5)-P5)] (Cp(BIG)=C5(4-nBuC6H4)5), the novel multishell aggregate [{Cp(BIG)Fe(η(5:2:1:1:1:1:1)-P5)}12(CuBr)92] is obtained. It shows topological analogy to the theoretically predicted I-C140 fullerene molecule. The spherical cluster was comprehensively characterized by various methods in solution and in the solid state. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Microhydration and the Enhanced Acidity of Free Radicals.

PubMed

Walton, John C

2018-02-14

Recent theoretical research employing a continuum solvent model predicted that radical centers would enhance the acidity (RED-shift) of certain proton-donor molecules. Microhydration studies employing a DFT method are reported here with the aim of establishing the effect of the solvent micro-structure on the acidity of radicals with and without RED-shifts. Microhydration cluster structures were obtained for carboxyl, carboxy-ethynyl, carboxy-methyl, and hydroperoxyl radicals. The numbers of water molecules needed to induce spontaneous ionization were determined. The hydration clusters formed primarily round the CO₂ units of the carboxylate-containing radicals. Only 4 or 5 water molecules were needed to induce ionization of carboxyl and carboxy-ethynyl radicals, thus corroborating their large RED-shifts.

Casein Aggregates Built Step-by-Step on Charged Polyelectrolyte Film Surfaces Are Calcium Phosphate-cemented*

PubMed Central

Nagy, Krisztina; Pilbat, Ana-Maria; Groma, Géza; Szalontai, Balázs; Cuisinier, Frédéric J. G.

2010-01-01

The possible mechanism of casein aggregation and micelle buildup was studied in a new approach by letting α-casein adsorb from low concentration (0.1 mg·ml−1) solutions onto the charged surfaces of polyelectrolyte films. It was found that α-casein could adsorb onto both positively and negatively charged surfaces. However, only when its negative phosphoseryl clusters remained free, i.e. when it adsorbed onto a negative surface, could calcium phosphate (CaP) nanoclusters bind to the casein molecules. Once the CaP clusters were in place, step-by-step building of multilayered casein architectures became possible. The presence of CaP was essential; neither Ca2+ nor phosphate could alone facilitate casein aggregation. Thus, it seems that CaP is the organizing motive in the casein micelle formation. Atomic force microscopy revealed that even a single adsorbed casein layer was composed of very small (in the range of tens of nanometers) spherical forms. The stiffness of the adsorbed casein layer largely increased in the presence of CaP. On this basis, we can imagine that casein micelles emerge according to the following scheme. The amphipathic casein monomers aggregate into oligomers via hydrophobic interactions even in the absence of CaP. Full scale, CaP-carrying micelles could materialize by interlocking these casein oligomers with CaP nanoclusters. Such a mechanism would not contradict former experimental results and could offer a synthesis between the submicelle and the block copolymer models of casein micelles. PMID:20921229

Route to the Smallest Doped Semiconductor: Mn(2+)-Doped (CdSe)13 Clusters.

PubMed

Yang, Jiwoong; Fainblat, Rachel; Kwon, Soon Gu; Muckel, Franziska; Yu, Jung Ho; Terlinden, Hendrik; Kim, Byung Hyo; Iavarone, Dino; Choi, Moon Kee; Kim, In Young; Park, Inchul; Hong, Hyo-Ki; Lee, Jihwa; Son, Jae Sung; Lee, Zonghoon; Kang, Kisuk; Hwang, Seong-Ju; Bacher, Gerd; Hyeon, Taeghwan

2015-10-14

Doping semiconductor nanocrystals with magnetic transition-metal ions has attracted fundamental interest to obtain a nanoscale dilute magnetic semiconductor, which has unique spin exchange interaction between magnetic spin and exciton. So far, the study on the doped semiconductor NCs has usually been conducted with NCs with larger than 2 nm because of synthetic challenges. Herein, we report the synthesis and characterization of Mn(2+)-doped (CdSe)13 clusters, the smallest doped semiconductors. In this study, single-sized doped clusters are produced in large scale. Despite their small size, these clusters have semiconductor band structure instead of that of molecules. Surprisingly, the clusters show multiple excitonic transitions with different magneto-optical activities, which can be attributed to the fine structure splitting. Magneto-optically active states exhibit giant Zeeman splittings up to elevated temperatures (128 K) with large g-factors of 81(±8) at 4 K. Our results present a new synthetic method for doped clusters and facilitate the understanding of doped semiconductor at the boundary of molecules and quantum nanostructure.

A [4Fe-4S]-Fe(CO)(CN)-l-cysteine intermediate is the first organometallic precursor in [FeFe] hydrogenase H-cluster bioassembly

NASA Astrophysics Data System (ADS)

Rao, Guodong; Tao, Lizhi; Suess, Daniel L. M.; Britt, R. David

2018-05-01

Biosynthesis of the [FeFe] hydrogenase active site (the 'H-cluster') requires the interplay of multiple proteins and small molecules. Among them, the radical S-adenosylmethionine enzyme HydG, a tyrosine lyase, has been proposed to generate a complex that contains an Fe(CO)2(CN) moiety that is eventually incorporated into the H-cluster. Here we describe the characterization of an intermediate in the HydG reaction: a [4Fe-4S][(Cys)Fe(CO)(CN)] species, 'Complex A', in which a CO, a CN- and a cysteine (Cys) molecule bind to the unique 'dangler' Fe site of the auxiliary [5Fe-4S] cluster of HydG. The identification of this intermediate—the first organometallic precursor to the H-cluster—validates the previously hypothesized HydG reaction cycle and provides a basis for elucidating the biosynthetic origin of other moieties of the H-cluster.

Quantum structural fluctuation in para-hydrogen clusters revealed by the variational path integral method

NASA Astrophysics Data System (ADS)

Miura, Shinichi

2018-03-01

In this paper, the ground state of para-hydrogen clusters for size regime N ≤ 40 has been studied by our variational path integral molecular dynamics method. Long molecular dynamics calculations have been performed to accurately evaluate ground state properties. The chemical potential of the hydrogen molecule is found to have a zigzag size dependence, indicating the magic number stability for the clusters of the size N = 13, 26, 29, 34, and 39. One-body density of the hydrogen molecule is demonstrated to have a structured profile, not a melted one. The observed magic number stability is examined using the inherent structure analysis. We also have developed a novel method combining our variational path integral hybrid Monte Carlo method with the replica exchange technique. We introduce replicas of the original system bridging from the structured to the melted cluster, which is realized by scaling the potential energy of the system. Using the enhanced sampling method, the clusters are demonstrated to have the structured density profile in the ground state.

Quantum structural fluctuation in para-hydrogen clusters revealed by the variational path integral method.

PubMed

Miura, Shinichi

2018-03-14

In this paper, the ground state of para-hydrogen clusters for size regime N ≤ 40 has been studied by our variational path integral molecular dynamics method. Long molecular dynamics calculations have been performed to accurately evaluate ground state properties. The chemical potential of the hydrogen molecule is found to have a zigzag size dependence, indicating the magic number stability for the clusters of the size N = 13, 26, 29, 34, and 39. One-body density of the hydrogen molecule is demonstrated to have a structured profile, not a melted one. The observed magic number stability is examined using the inherent structure analysis. We also have developed a novel method combining our variational path integral hybrid Monte Carlo method with the replica exchange technique. We introduce replicas of the original system bridging from the structured to the melted cluster, which is realized by scaling the potential energy of the system. Using the enhanced sampling method, the clusters are demonstrated to have the structured density profile in the ground state.

IR + VUV double resonance spectroscopy and extended density functional theory studies of ketone solvation by alcohol: 2-butanone·(methanol)n, n = 1-4 clusters.

PubMed

Shin, Joong-Won; Bernstein, Elliot R

2017-09-28

Infrared plus vacuum ultraviolet (IR + VUV) photoionization vibrational spectroscopy of 2-butanone/methanol clusters [MEK·(MeOH) n , n = 1-4] is performed to explore structures associated with hydrogen bonding of MeOH molecules to the carbonyl functional group of the ketone. IR spectra and X3LYP/6-31++G(d,p) calculations show that multiple isomers of MEK·(MeOH) n are generated in the molecular beam as a result of several hydrogen bonding sites available to the clusters throughout the size range investigated. Isomer interconversion involving solvating MeOH rearrangement should probably occur for n = 1 and 2. The mode energy for a hydrogen bonded OH stretching transition gradually redshifts as the cluster size increases. Calculations suggest that the n = 3 cluster isomers adopt structures in which the MEK molecule is inserted into the cyclic MeOH hydrogen bond network. In larger structures, the cyclic network may be preserved.

Role of size, composition and substrate in controlling the reactivity of α(0001)-Al2O3 supported AgnAum (n + m = 2 - 4) alloy clusters for CO-oxidation: A comprehensive density functional study

NASA Astrophysics Data System (ADS)

Singh, Akansha; Majumder, Chiranjib; Sen, Prasenjit

2018-03-01

Catalytic efficiency of gas phase and alumina-supported bimetallic AgnAum (n + m = 2 - 4) alloy clusters is studied using density functional methods As a pre-requite, adsorption of O2 and CO molecules, and co-adsorption of both molecules on these clusters are studied in detail. O2 and CO are co-adsorbed on nearby sites on the gas phase tetramer clusters Ag2Au2 and Ag3Au. But their catalytic efficiency is hindered by large barriers (1.55 eV and 1.44 eV, respectively) to the breaking of Osbnd O bond. Among the deposited clusters, Ag2Au and AgAu2 have O2 and CO co-adsorbed on nearby locations. Of these two, Ag2Au has a lower kinetic barrier for subsequent CO2 formation. Thus Ag2Au looks the most promising candidate.

Exploring the Counteracting Mechanism of Trehalose on Urea Conferred Protein Denaturation: A Molecular Dynamics Simulation Study.

PubMed

Paul, Subrata; Paul, Sandip

2015-07-30

To provide the underlying mechanism of the inhibiting effect of trehalose on the urea denatured protein, we perform classical molecular dynamics simulations of N-methylacetamide (NMA) in aqueous urea and/or trehalose solution. The site-site radial distribution functions and hydrogen bond properties indicate in binary urea solution the replacement of NMA-water hydrogen bonds by NMA-urea hydrogen bonds. On the other hand, in ternary urea and trehalose solution, trehalose does not replace the NMA-urea hydrogen bonds significantly; rather, it forms hydrogen bonds with the NMA molecule. The calculation of a preferential interaction parameter shows that, at the NMA surface, trehalose molecules are preferred and the preference for urea decreases slightly in ternary solution with respect to the binary solution. The exclusion of urea molecules in the ternary urea-NMA-trehalose system causes alleviation in van der Waals interaction energy between urea and NMA molecules. Our findings also reveal the following: (a) trehalose and urea induced second shell collapse of water structure, (b) a reduction in the mean trehalose cluster size in ternary solution, and (c) slowing down of translational motion of solution species in the presence of osmolytes. Implications of these results for the molecular explanations of the counteracting mechanism of trehalose on urea induced protein denaturation are discussed.

Water droplet excess free energy determined by cluster mitosis using guided molecular dynamics

NASA Astrophysics Data System (ADS)

Lau, Gabriel V.; Hunt, Patricia A.; Müller, Erich A.; Jackson, George; Ford, Ian J.

2015-12-01

Atmospheric aerosols play a vital role in affecting climate by influencing the properties and lifetimes of clouds and precipitation. Understanding the underlying microscopic mechanisms involved in the nucleation of aerosol droplets from the vapour phase is therefore of great interest. One key thermodynamic quantity in nucleation is the excess free energy of cluster formation relative to that of the saturated vapour. In our current study, the excess free energy is extracted for clusters of pure water modelled with the TIP4P/2005 intermolecular potential using a method based on nonequilibrium molecular dynamics and the Jarzynski relation. The change in free energy associated with the "mitosis" or division of a cluster of N water molecules into two N/2 sub-clusters is evaluated. This methodology is an extension of the disassembly procedure used recently to calculate the excess free energy of argon clusters [H. Y. Tang and I. J. Ford, Phys. Rev. E 91, 023308 (2015)]. Our findings are compared to the corresponding excess free energies obtained from classical nucleation theory (CNT) as well as internally consistent classical theory (ICCT). The values of the excess free energy that we obtain with the mitosis method are consistent with CNT for large cluster sizes but for the smallest clusters, the results tend towards ICCT; for intermediate sized clusters, we obtain values between the ICCT and CNT predictions. Furthermore, the curvature-dependent surface tension which can be obtained by regarding the clusters as spherical droplets of bulk density is found to be a monotonically increasing function of cluster size for the studied range. The data are compared to other values reported in the literature, agreeing qualitatively with some but disagreeing with the values determined by Joswiak et al. [J. Phys. Chem. Lett. 4, 4267 (2013)] using a biased mitosis approach; an assessment of the differences is the main motivation for our current study.

Water droplet excess free energy determined by cluster mitosis using guided molecular dynamics

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

Lau, Gabriel V.; Müller, Erich A.; Jackson, George

Atmospheric aerosols play a vital role in affecting climate by influencing the properties and lifetimes of clouds and precipitation. Understanding the underlying microscopic mechanisms involved in the nucleation of aerosol droplets from the vapour phase is therefore of great interest. One key thermodynamic quantity in nucleation is the excess free energy of cluster formation relative to that of the saturated vapour. In our current study, the excess free energy is extracted for clusters of pure water modelled with the TIP4P/2005 intermolecular potential using a method based on nonequilibrium molecular dynamics and the Jarzynski relation. The change in free energy associatedmore » with the “mitosis” or division of a cluster of N water molecules into two N/2 sub-clusters is evaluated. This methodology is an extension of the disassembly procedure used recently to calculate the excess free energy of argon clusters [H. Y. Tang and I. J. Ford, Phys. Rev. E 91, 023308 (2015)]. Our findings are compared to the corresponding excess free energies obtained from classical nucleation theory (CNT) as well as internally consistent classical theory (ICCT). The values of the excess free energy that we obtain with the mitosis method are consistent with CNT for large cluster sizes but for the smallest clusters, the results tend towards ICCT; for intermediate sized clusters, we obtain values between the ICCT and CNT predictions. Furthermore, the curvature-dependent surface tension which can be obtained by regarding the clusters as spherical droplets of bulk density is found to be a monotonically increasing function of cluster size for the studied range. The data are compared to other values reported in the literature, agreeing qualitatively with some but disagreeing with the values determined by Joswiak et al. [J. Phys. Chem. Lett. 4, 4267 (2013)] using a biased mitosis approach; an assessment of the differences is the main motivation for our current study.« less

Helium segregation on surfaces of plasma-exposed tungsten

DOE PAGES

Maroudas, Dimitrios; Blondel, Sophie; Hu, Lin; ...

2016-01-21

Here we report a hierarchical multi-scale modeling study of implanted helium segregation on surfaces of tungsten, considered as a plasma facing component in nuclear fusion reactors. We employ a hierarchy of atomic-scale simulations based on a reliable interatomic interaction potential, including molecular-statics simulations to understand the origin of helium surface segregation, targeted molecular-dynamics (MD) simulations of near-surface cluster reactions, and large-scale MD simulations of implanted helium evolution in plasma-exposed tungsten. We find that small, mobile He-n (1 <= n <= 7) clusters in the near-surface region are attracted to the surface due to an elastic interaction force that provides themore » thermodynamic driving force for surface segregation. Elastic interaction force induces drift fluxes of these mobile Hen clusters, which increase substantially as the migrating clusters approach the surface, facilitating helium segregation on the surface. Moreover, the clusters' drift toward the surface enables cluster reactions, most importantly trap mutation, in the near-surface region at rates much higher than in the bulk material. Moreover, these near-surface cluster dynamics have significant effects on the surface morphology, near-surface defect structures, and the amount of helium retained in the material upon plasma exposure. We integrate the findings of such atomic-scale simulations into a properly parameterized and validated spatially dependent, continuum-scale reaction-diffusion cluster dynamics model, capable of predicting implanted helium evolution, surface segregation, and its near-surface effects in tungsten. This cluster-dynamics model sets the stage for development of fully atomistically informed coarse-grained models for computationally efficient simulation predictions of helium surface segregation, as well as helium retention and surface morphological evolution, toward optimal design of plasma facing components.« less

The interplay of covalency, hydrogen bonding, and dispersion leads to a long range chiral network: The example of 2-butanol

NASA Astrophysics Data System (ADS)

Liriano, Melissa L.; Carrasco, Javier; Lewis, Emily A.; Murphy, Colin J.; Lawton, Timothy J.; Marcinkowski, Matthew D.; Therrien, Andrew J.; Michaelides, Angelos; Sykes, E. Charles H.

2016-03-01

The assembly of complex structures in nature is driven by an interplay between several intermolecular interactions, from strong covalent bonds to weaker dispersion forces. Understanding and ultimately controlling the self-assembly of materials requires extensive study of how these forces drive local nanoscale interactions and how larger structures evolve. Surface-based self-assembly is particularly amenable to modeling and measuring these interactions in well-defined systems. This study focuses on 2-butanol, the simplest aliphatic chiral alcohol. 2-butanol has recently been shown to have interesting properties as a chiral modifier of surface chemistry; however, its mode of action is not fully understood and a microscopic understanding of the role non-covalent interactions play in its adsorption and assembly on surfaces is lacking. In order to probe its surface properties, we employed high-resolution scanning tunneling microscopy and density functional theory (DFT) simulations. We found a surprisingly rich degree of enantiospecific adsorption, association, chiral cluster growth and ultimately long range, highly ordered chiral templating. Firstly, the chiral molecules acquire a second chiral center when adsorbed to the surface via dative bonding of one of the oxygen atom lone pairs. This interaction is controlled via the molecule's intrinsic chiral center leading to monomers of like chirality, at both chiral centers, adsorbed on the surface. The monomers then associate into tetramers via a cyclical network of hydrogen bonds with an opposite chirality at the oxygen atom. The evolution of these square units is surprising given that the underlying surface has a hexagonal symmetry. Our DFT calculations, however, reveal that the tetramers are stable entities that are able to associate with each other by weaker van der Waals interactions and tessellate in an extended square network. This network of homochiral square pores grows to cover the whole Au(111) surface. Our data reveal that the chirality of a simple alcohol can be transferred to its surface binding geometry, drive the directionality of hydrogen-bonded networks and ultimately extended structure. Furthermore, this study provides the first microscopic insight into the surface properties of this important chiral modifier and provides a well-defined system for studying the network's enantioselective interaction with other molecules.

Discovery of a Phosphonoacetic Acid Derived Natural Product by Pathway Refactoring.

PubMed

Freestone, Todd S; Ju, Kou-San; Wang, Bin; Zhao, Huimin

2017-02-17

The activation of silent natural product gene clusters is a synthetic biology problem of great interest. As the rate at which gene clusters are identified outpaces the discovery rate of new molecules, this unknown chemical space is rapidly growing, as too are the rewards for developing technologies to exploit it. One class of natural products that has been underrepresented is phosphonic acids, which have important medical and agricultural uses. Hundreds of phosphonic acid biosynthetic gene clusters have been identified encoding for unknown molecules. Although methods exist to elicit secondary metabolite gene clusters in native hosts, they require the strain to be amenable to genetic manipulation. One method to circumvent this is pathway refactoring, which we implemented in an effort to discover new phosphonic acids from a gene cluster from Streptomyces sp. strain NRRL F-525. By reengineering this cluster for expression in the production host Streptomyces lividans, utility of refactoring is demonstrated with the isolation of a novel phosphonic acid, O-phosphonoacetic acid serine, and the characterization of its biosynthesis. In addition, a new biosynthetic branch point is identified with a phosphonoacetaldehyde dehydrogenase, which was used to identify additional phosphonic acid gene clusters that share phosphonoacetic acid as an intermediate.

Aqueous solvation of Mg(ii) and Ca(ii): A Born-Oppenheimer molecular dynamics study of microhydrated gas phase clusters

NASA Astrophysics Data System (ADS)

León-Pimentel, C. I.; Amaro-Estrada, J. I.; Hernández-Cobos, J.; Saint-Martin, H.; Ramírez-Solís, A.

2018-04-01

The hydration features of [Mg(H2O)n ] 2 + and [Ca(H2O)n ] 2 + clusters with n = 3-6, 8, 18, and 27 were studied by means of Born-Oppenheimer molecular dynamics simulations at the B3LYP/6-31+G** level of theory. For both ions, it is energetically more favorable to have all water molecules in the first hydration shell when n ≤ 6, but stable lower coordination average structures with one water molecule not directly interacting with the ion were found for Mg2+ at room temperature, showing signatures of proton transfer events for the smaller cation but not for the larger one. A more rigid octahedral-type structure for Mg2+ than for Ca2+ was observed in all simulations, with no exchange of water molecules to the second hydration shell. Significant thermal effects on the average structure of clusters were found: while static optimizations lead to compact, spherically symmetric hydration geometries, the effects introduced by finite-temperature dynamics yield more prolate configurations. The calculated vibrational spectra are in agreement with infrared spectroscopy results. Previous studies proposed an increase in the coordination number (CN) from six to eight water molecules for [Ca(H2O)n ] 2 + clusters when n ≥ 12; however, in agreement with recent measurements of binding energies, no transition to a larger CN was found when n > 8. Moreover, the excellent agreement found between the calculated extended X-ray absorption fine structure spectroscopy spectra for the larger cluster and the experimental data of the aqueous solution supports a CN of six for Ca2+.

Perspectives on the energy landscape of Au-Cl binary systems from the structural phase diagram of AuxCly (x + y = 20).

PubMed

Tian, Zhimei; Cheng, Longjiu

2015-05-28

Ligand-protected gold (Au-L) nanoclusters have attracted much attention, where the reported electronic and geometric structures show great diversity. To give a direct and overall view of the energy landscape of Au-L binary systems, the AuxCly (x + y = 20) system is taken as a test case. By intensive global search of the potential energy surface at the level of density functional theory, a diverse set of global minima and low-lying isomers are found at each composition, and the structural phase diagram is obtained. The unbiased global search is carried out using the method combining the genetic algorithm with the TPSS functional. At x = 10 with the stoichiometric ratio of Au and Cl (1 : 1), the cluster presents a catenane structure. When x is in the range of 11-20, the clusters are Au-rich, and the Au-Cl system can be viewed as Cl-protected gold nanoclusters, where the gold cores consist of superatoms, superatom networks, or superatomic molecules in electronic structures. At x = 11-15, the gold cores consist of Au3, Au4 and Au5 2e-superatoms protected by staple motifs. At x = 16-20, the clusters are pyramidal superatomic molecules with one Au16 superatom core bonding with the four vertical atoms (Au or Cl). When x is in the scope of 9-5, the clusters are Cl-rich, and the 5d electrons of Au participate in bonding, resulting in high multiplicities. The Au-Cl binary system shows great diversity and flexibility in electronic and geometric structures, and there are corresponding structures to most of the experimentally produced Au-L nanoclusters in our structural phase diagram. We believe that the structural phase diagram gives an overall perspective on the universe of Au-L nanoclusters.

An orientation analysis method for protein immobilized on quantum dot particles

NASA Astrophysics Data System (ADS)

Aoyagi, Satoka; Inoue, Masae

2009-11-01

The evaluation of orientation of biomolecules immobilized on nanodevices is crucial for the development of high performance devices. Such analysis requires ultra high sensitivity so as to be able to detect less than one molecular layer on a device. Time-of-flight secondary ion mass spectrometry (TOF-SIMS) has sufficient sensitivity to evaluate the uppermost surface structure of a single molecular layer. The objective of this study is to develop an orientation analysis method for proteins immobilized on nanomaterials such as quantum dot particles, and to evaluate the orientation of streptavidin immobilized on quantum dot particles by means of TOF-SIMS. In order to detect fragment ions specific to the protein surface, a monoatomic primary ion source (Ga +) and a cluster ion source (Au 3+) were employed. Streptavidin-immobilized quantum dot particles were immobilized on aminosilanized ITO glass plates at amino groups by covalent bonding. The reference samples streptavidin directly immobilized on ITO plates were also prepared. All samples were dried with a freeze dryer before TOF-SIMS measurement. The positive secondary ion spectra of each sample were obtained using TOF-SIMS with Ga + and Au 3+, respectively, and then they were compared so as to characterize each sample and detect the surface structure of the streptavidin immobilized with the biotin-immobilized quantum dots. The chemical structures of the upper surface of the streptavidin molecules immobilized on the quantum dot particles were evaluated with TOF-SIMS spectra analysis. The indicated surface side of the streptavidin molecules immobilized on the quantum dots includes the biotin binding site.

Formation rates, stability and reactivity of sulfuric acid - amine clusters predicted by computational chemistry

NASA Astrophysics Data System (ADS)

Kurtén, Theo; Ortega, Ismael; Kupiainen, Oona; Olenius, Tinja; Loukonen, Ville; Reiman, Heidi; McGrath, Matthew; Vehkamäki, Hanna

2013-04-01

Despite the importance of atmospheric particle formation for both climate and air quality, both experiments and non-empirical models using e.g. sulfuric acid, ammonia and water as condensing vapors have so far been unable to reproduce atmospheric observations using realistic trace gas concentrations. Recent experimental and theoretical evidence has shown that this mystery is likely resolved by amines. Combining first-principles evaporation rates for sulfuric acid - dimethylamine clusters with cluster kinetic modeling, we show that even sub-ppt concentrations of amines, together with atmospherically realistic concentrations of sulfuric acid, result in formation rates close to those observed in the atmosphere. Our simulated cluster formation rates are also close to, though somewhat larger than, those measured at the CLOUD experiment in CERN for both sulfuric acid - ammonia and sulfuric acid - dimethylamine systems. A sensitivity analysis indicates that the remaining discrepancy for the sulfuric acid - amine particle formation rates is likely caused by steric hindrances to cluster formation (due to alkyl groups of the amine molecules) rather than by significant errors in the evaporation rates. First-principles molecular dynamic and reaction kinetic modeling shed further light on the microscopic physics and chemistry of sulfuric acid - amine clusters. For example, while the number and type of hydrogen bonds in the clusters typically reach their equilibrium values on a picosecond timescale, and the overall bonding patterns predicted by traditional "static" quantum chemical calculations seem to be stable, the individual atoms participating in the hydrogen bonds continuously change at atmospherically realistic temperatures. From a chemical reactivity perspective, we have also discovered a surprising phenomenon: clustering with sulfuric acid molecules slightly increases the activation energy required for the abstraction of alkyl hydrogens from amine molecules. This implies that the oxidation rate of amines by OH and possibly other oxidants may be decreased by clustering, thus prolonging the chemical lifetime of amines in the air.

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

PubMed Central

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

Electric dipole moments of nanosolvated acid molecules in water clusters.

PubMed

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.

Accounting for Limited Detection Efficiency and Localization Precision in Cluster Analysis in Single Molecule Localization Microscopy

PubMed Central

Shivanandan, Arun; Unnikrishnan, Jayakrishnan; Radenovic, Aleksandra

2015-01-01

Single Molecule Localization Microscopy techniques like PhotoActivated Localization Microscopy, with their sub-diffraction limit spatial resolution, have been popularly used to characterize the spatial organization of membrane proteins, by means of quantitative cluster analysis. However, such quantitative studies remain challenged by the techniques’ inherent sources of errors such as a limited detection efficiency of less than 60%, due to incomplete photo-conversion, and a limited localization precision in the range of 10 – 30nm, varying across the detected molecules, mainly depending on the number of photons collected from each. We provide analytical methods to estimate the effect of these errors in cluster analysis and to correct for them. These methods, based on the Ripley’s L(r) – r or Pair Correlation Function popularly used by the community, can facilitate potentially breakthrough results in quantitative biology by providing a more accurate and precise quantification of protein spatial organization. PMID:25794150

A new method to prepare colloids of size-controlled clusters from a matrix assembly cluster source

NASA Astrophysics Data System (ADS)

Cai, Rongsheng; Jian, Nan; Murphy, Shane; Bauer, Karl; Palmer, Richard E.

2017-05-01

A new method for the production of colloidal suspensions of physically deposited clusters is demonstrated. A cluster source has been used to deposit size-controlled clusters onto water-soluble polymer films, which are then dissolved to produce colloidal suspensions of clusters encapsulated with polymer molecules. This process has been demonstrated using different cluster materials (Au and Ag) and polymers (polyvinylpyrrolidone, polyvinyl alcohol, and polyethylene glycol). Scanning transmission electron microscopy of the clusters before and after colloidal dispersion confirms that the polymers act as stabilizing agents. We propose that this method is suitable for the production of biocompatible colloids of ultraprecise clusters.

The hydration structure of the heavy-alkalines Rb+ and Cs+ through molecular dynamics and X-ray absorption spectroscopy: surface clusters and eccentricity.

PubMed

Caralampio, Daniel Z; Martínez, José M; Pappalardo, Rafael R; Marcos, Enrique Sánchez

2017-11-01

Physicochemical properties of the two heaviest stable alkaline cations, Rb + and Cs + , in water have been examined from classical molecular dynamics (MD) simulations. Alkaline cation-water intermolecular potentials have been built from ab initio interaction energies of [M(H 2 O) n ] + clusters. Unlike in the case of other monatomic metal cations, the sampling needed the inclusion of surface clusters to properly describe the interactions. The first coordination shell is found at an average M-O distance of 2.87 Å and 3.12 Å for Rb + and Cs + , respectively, with coordination numbers of 8 and 10. Structural, dynamical and energetic properties are discussed on the basis of the delicate compromise among the ion-water and water-water interactions which contribute almost on the same foot to the definition of the solvent structure around the ions. A significant asymmetry is detected in the Rb + and Cs + first hydration shell. Reorientational times of first-shell water molecules for Cs + support a clear structure-breaking nature for this cation, whereas the Rb + values do not differ from pure water behavior. Experimental EXAFS and XANES spectra have been compared to simulated ones, obtained by means of application of the FEFF code to a set of statistically significant structures taken from the MD simulations. Due to the presence of multi-excitations in the absorption spectra, theoretical-experimental agreement for the EXAFS spectra is reached when the multi-excitations are removed from the experimental spectra.

Preparation and characterization of chemically defined oligomers of rabbit immunoglobulin G molecules for the complement binding studies.

PubMed Central

Wright, J K; Tschopp, J; Jaton, J C

1980-01-01

Pure dimers, trimers, tetramers and pentamers of rabbit non-immune IgG (immunoglobulin G) or antibody IgG were prepared by polymerization in the presence of the bifunctional cross-linking reagent dithiobis (succinimidylpropionate). Oligomerization was performed either in the presence of polysaccharide antigen and specific monomeric antibody (method A) or by random cross-linking of non-immune rabbit IgG in the absence of antigen (method B). By repeated gel-filtration chromatography, samples prepared by both methods exhibited a single band in analytical sodium dodecyl sulphate/polyacrylamide-gel electrophoresis. The electrophoretic mobilities of samples prepared by method A were slightly greater than those for the corresponding samples prepared by method B. This might suggest a role played by antigen in the orientation of IgG molecules within the clusters, which may be more compact than those formed by random cross-linking. The average numbers of cross-linker molecules per oligomer varied between 3 and 6 for clusters made by method A and between 1 and 3 for clusters made by method B. Ultracentrifugal analyses of the oligomers yielded sedimentation coefficients (S20,w) of 9.6S for the dimer, 11.2S for the trimer, 13.6S for the tetramer and 16.1S for the pentamer. Comparison of the observed sedimentation coefficients with those predicted by various hydrodynamic models suggested these oligomers possessed open and linear structures. Reduction of the cross-linking molecules converted oligomers into monomeric species of IgG. C.d. spectra of some oligomers studied in the range 200-250 nm were essentially the same as that of monomeric IgG molecules, thus strongly suggesting no major conformation changes in IgG molecules within clusters. These oligomers were found to be stable for up to 2 months when stored at -70 degrees C. Images Fig. 1. Fig. 4. PMID:7188424

Isolation and Spectroscopic Characterization of Reactive Species in Atmospheric and Interstellar Reactions

NASA Astrophysics Data System (ADS)

Relph, Rachael A.

2011-12-01

A critical element to the study of chemical reactions is the characterization of reaction intermediates. Methods have been developed to isolate these transient species in the gas phase and when combined with infrared spectroscopy have proven to be excellent tools for determining the structure and reactivity of key intermediates. The studies presented here exploit these technologies to better understand the chemistry of species involved in atmospheric and interstellar reactions. An excellent example of their utility is in the study of the formation of proton hydrates and HONO in the upper atmosphere by sequential addition of water molecules onto the nitrosonium ion. This reaction only proceeds to products after addition of the fourth water molecule, and isolation and characterization of the intermediate trihydrate, NO+(H 2O)3, shows that this species is formed in three isomeric forms, each with a different water network that controls the degree of bond formation between the nitrosonium ion and an activated water molecule. Many isomeric structures are also seen in the clustering reactions of acetylene which may be a mechanism for the formation of benzene cation in interstellar space. The spectroscopy of the trimer, (C2H2)3 + indicates that this species exists in two major isomer classes; covalent forms, one of which may be benzene, and an ion-molecule complex, comprised of a loosely bound acetylene on a dimer core. Interestingly, this dimer core is different from the cyclobutadiene-like structure observed in dimerized acetylene, and proves to be a robust species on the potential energy surface as it survives further clustering events. Two structural isomers of CO3 -and NO3 - are also investigated, and found to have drastically different infrared spectra which are analyzed in the context of their electronic structure. Isomers in these systems are prepared under different expansion conditions which accounts for their unique spectral signatures.

Live-cell imaging reveals the dynamics and function of single-telomere TERRA molecules in cancer cells.

PubMed

Avogaro, Laura; Querido, Emmanuelle; Dalachi, Myriam; Jantsch, Michael F; Chartrand, Pascal; Cusanelli, Emilio

2018-04-16

Telomeres cap the ends of eukaryotic chromosomes, protecting them from degradation and erroneous recombination events which may lead to genome instability. Telomeres are transcribed giving rise to telomeric repeat-containing RNAs, called TERRA. The TERRA long noncoding RNAs have been proposed to play important roles in telomere biology, including heterochromatin formation and telomere length homeostasis. While TERRA RNAs are predominantly nuclear and localize at telomeres, little is known about the dynamics and function of TERRA molecules expressed from individual telomeres. Herein, we developed an assay to image endogenous TERRA molecules expressed from a single telomere in living human cancer cells. We show that single-telomere TERRA can be detected as TERRA RNA single particles which freely diffuse within the nucleus. Furthermore, TERRA molecules aggregate forming TERRA clusters. Three-dimensional size distribution and single particle tracking analyses revealed distinct sizes and dynamics for TERRA RNA single particles and clusters. Simultaneous time lapse confocal imaging of TERRA particles and telomeres showed that TERRA clusters transiently co-localize with telomeres. Finally, we used chemically modified antisense oligonucleotides to deplete TERRA molecules expressed from a single telomere. Single-telomere TERRA depletion resulted in increased DNA damage at telomeres and elsewhere in the genome. These results suggest that single-telomere TERRA transcripts participate in the maintenance of genomic integrity in human cancer cells.

BiP clustering facilitates protein folding in the endoplasmic reticulum.

PubMed

Griesemer, Marc; Young, Carissa; Robinson, Anne S; Petzold, Linda

2014-07-01

The chaperone BiP participates in several regulatory processes within the endoplasmic reticulum (ER): translocation, protein folding, and ER-associated degradation. To facilitate protein folding, a cooperative mechanism known as entropic pulling has been proposed to demonstrate the molecular-level understanding of how multiple BiP molecules bind to nascent and unfolded proteins. Recently, experimental evidence revealed the spatial heterogeneity of BiP within the nuclear and peripheral ER of S. cerevisiae (commonly referred to as 'clusters'). Here, we developed a model to evaluate the potential advantages of accounting for multiple BiP molecules binding to peptides, while proposing that BiP's spatial heterogeneity may enhance protein folding and maturation. Scenarios were simulated to gauge the effectiveness of binding multiple chaperone molecules to peptides. Using two metrics: folding efficiency and chaperone cost, we determined that the single binding site model achieves a higher efficiency than models characterized by multiple binding sites, in the absence of cooperativity. Due to entropic pulling, however, multiple chaperones perform in concert to facilitate the resolubilization and ultimate yield of folded proteins. As a result of cooperativity, multiple binding site models used fewer BiP molecules and maintained a higher folding efficiency than the single binding site model. These insilico investigations reveal that clusters of BiP molecules bound to unfolded proteins may enhance folding efficiency through cooperative action via entropic pulling.

Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy.

PubMed

Zhao, Ziqing W; Roy, Rahul; Gebhardt, J Christof M; Suter, David M; Chapman, Alec R; Xie, X Sunney

2014-01-14

Superresolution microscopy based on single-molecule centroid determination has been widely applied to cellular imaging in recent years. However, quantitative imaging of the mammalian nucleus has been challenging due to the lack of 3D optical sectioning methods for normal-sized cells, as well as the inability to accurately count the absolute copy numbers of biomolecules in highly dense structures. Here we report a reflected light-sheet superresolution microscopy method capable of imaging inside the mammalian nucleus with superior signal-to-background ratio as well as molecular counting with single-copy accuracy. Using reflected light-sheet superresolution microscopy, we probed the spatial organization of transcription by RNA polymerase II (RNAP II) molecules and quantified their global extent of clustering inside the mammalian nucleus. Spatiotemporal clustering analysis that leverages on the blinking photophysics of specific organic dyes showed that the majority (>70%) of the transcription foci originate from single RNAP II molecules, and no significant clustering between RNAP II molecules was detected within the length scale of the reported diameter of "transcription factories." Colocalization measurements of RNAP II molecules equally labeled by two spectrally distinct dyes confirmed the primarily unclustered distribution, arguing against a prevalent existence of transcription factories in the mammalian nucleus as previously proposed. The methods developed in our study pave the way for quantitative mapping and stoichiometric characterization of key biomolecular species deep inside mammalian cells.

Renormalized coupled cluster approaches in the cluster-in-molecule framework: predicting vertical electron binding energies of the anionic water clusters (H2O)(n)(-).

PubMed

Xu, Peng; Gordon, Mark S

2014-09-04

Anionic water clusters are generally considered to be extremely challenging to model using fragmentation approaches due to the diffuse nature of the excess electron distribution. The local correlation coupled cluster (CC) framework cluster-in-molecule (CIM) approach combined with the completely renormalized CR-CC(2,3) method [abbreviated CIM/CR-CC(2,3)] is shown to be a viable alternative for computing the vertical electron binding energies (VEBE). CIM/CR-CC(2,3) with the threshold parameter ζ set to 0.001, as a trade-off between accuracy and computational cost, demonstrates the reliability of predicting the VEBE, with an average percentage error of ∼15% compared to the full ab initio calculation at the same level of theory. The errors are predominantly from the electron correlation energy. The CIM/CR-CC(2,3) approach provides the ease of a black-box type calculation with few threshold parameters to manipulate. The cluster sizes that can be studied by high-level ab initio methods are significantly increased in comparison with full CC calculations. Therefore, the VEBE computed by the CIM/CR-CC(2,3) method can be used as benchmarks for testing model potential approaches in small-to-intermediate-sized water clusters.

Stability investigation of a high number density Pt1/Fe2O3 single-atom catalyst under different gas environments by HAADF-STEM

NASA Astrophysics Data System (ADS)

Duan, Sibin; Wang, Rongming; Liu, Jingyue

2018-05-01

Catalysis by supported single metal atoms has demonstrated tremendous potential for practical applications due to their unique catalytic properties. Unless they are strongly anchored to the support surfaces, supported single atoms, however, are thermodynamically unstable, which poses a major obstacle for broad applications of single-atom catalysts (SACs). In order to develop strategies to improve the stability of SACs, we need to understand the intrinsic nature of the sintering processes of supported single metal atoms, especially under various gas environments that are relevant to important catalytic reactions. We report on the synthesis of high number density Pt1/Fe2O3 SACs using a facial strong adsorption method and the study of the mobility of these supported Pt single atoms at 250 °C under various gas environments that are relevant to CO oxidation, water–gas shift, and hydrogenation reactions. Under the oxidative gas environment, Fe2O3 supported Pt single atoms are stable even at high temperatures. The presence of either CO or H2 molecules in the gas environment, however, facilitates the movement of the Pt atoms. The strong interaction between CO and Pt weakens the binding between the Pt atoms and the support, facilitating the movement of the Pt single atoms. The dissociation of H2 molecules on the Pt atoms and their subsequent interaction with the oxygen species of the support surfaces dislodge the surface oxygen anchored Pt atoms, resulting in the formation of Pt clusters. The addition of H2O molecules to the CO or H2 significantly accelerates the sintering of the Fe2O3 supported Pt single atoms. An anchoring-site determined sintering mechanism is further proposed, which is related to the metal–support interaction.

Stability investigation of a high number density Pt1/Fe2O3 single-atom catalyst under different gas environments by HAADF-STEM.

PubMed

Duan, Sibin; Wang, Rongming; Liu, Jingyue

2018-05-18

Catalysis by supported single metal atoms has demonstrated tremendous potential for practical applications due to their unique catalytic properties. Unless they are strongly anchored to the support surfaces, supported single atoms, however, are thermodynamically unstable, which poses a major obstacle for broad applications of single-atom catalysts (SACs). In order to develop strategies to improve the stability of SACs, we need to understand the intrinsic nature of the sintering processes of supported single metal atoms, especially under various gas environments that are relevant to important catalytic reactions. We report on the synthesis of high number density Pt 1 /Fe 2 O 3 SACs using a facial strong adsorption method and the study of the mobility of these supported Pt single atoms at 250 °C under various gas environments that are relevant to CO oxidation, water-gas shift, and hydrogenation reactions. Under the oxidative gas environment, Fe 2 O 3 supported Pt single atoms are stable even at high temperatures. The presence of either CO or H 2 molecules in the gas environment, however, facilitates the movement of the Pt atoms. The strong interaction between CO and Pt weakens the binding between the Pt atoms and the support, facilitating the movement of the Pt single atoms. The dissociation of H 2 molecules on the Pt atoms and their subsequent interaction with the oxygen species of the support surfaces dislodge the surface oxygen anchored Pt atoms, resulting in the formation of Pt clusters. The addition of H 2 O molecules to the CO or H 2 significantly accelerates the sintering of the Fe 2 O 3 supported Pt single atoms. An anchoring-site determined sintering mechanism is further proposed, which is related to the metal-support interaction.

CO2 adsorption-assisted CH4 desorption on carbon models of coal surface: A DFT study

NASA Astrophysics Data System (ADS)

Xu, He; Chu, Wei; Huang, Xia; Sun, Wenjing; Jiang, Chengfa; Liu, Zhongqing

2016-07-01

Injection of CO2 into coal is known to improve the yields of coal-bed methane gas. However, the technology of CO2 injection-enhanced coal-bed methane (CO2-ECBM) recovery is still in its infancy with an unclear mechanism. Density functional theory (DFT) calculations were performed to elucidate the mechanism of CO2 adsorption-assisted CH4 desorption (AAD). To simulate coal surfaces, different six-ring aromatic clusters (2 × 2, 3 × 3, 4 × 4, 5 × 5, 6 × 6, and 7 × 7) were used as simplified graphene (Gr) carbon models. The adsorption and desorption of CH4 and/or CO2 on these carbon models were assessed. The results showed that a six-ring aromatic cluster model (4 × 4) can simulate the coal surface with limited approximation. The adsorption of CO2 onto these carbon models was more stable than that in the case of CH4. Further, the adsorption energies of single CH4 and CO2 in the more stable site were -15.58 and -18.16 kJ/mol, respectively. When two molecules (CO2 and CH4) interact with the surface, CO2 compels CH4 to adsorb onto the less stable site, with a resulting significant decrease in the adsorption energy of CH4 onto the surface of the carbon model with pre-adsorbed CO2. The Mulliken charges and electrostatic potentials of CH4 and CO2 adsorbed onto the surface of the carbon model were compared to determine their respective adsorption activities and changes. At the molecular level, our results showed that the adsorption of the injected CO2 promoted the desorption of CH4, the underlying mechanism of CO2-ECBM.

The effect of molecular shape on oligomerization of hydrophobic drugs: Molecular simulations of ciprofloxacin and nutlin

NASA Astrophysics Data System (ADS)

Li, Jianguo; Beuerman, Roger; Verma, Chandra

2018-03-01

Molecular aggregation plays a significant role in modulating the solubility, permeability, and bioactivity of drugs. The propensity to aggregate depends on hydrophobicity and on molecular shape. Molecular dynamics simulations coupled with enhanced sampling methods are used to explore the early stages of oligomerization of two drug molecules which have a strong aggregation propensity, but with contrasting molecule shapes: the antibiotic ciprofloxacin and the anticancer drug Nutlin-3A. The planar shape of ciprofloxacin induces the formation of stable oligomers at all cluster sizes. The aggregation of ciprofloxacin is driven by two-body interactions, and transferring one ciprofloxacin molecule to an existing cluster involves the desolvation of two faces and the concomitant hydrophobic interactions between the two faces; thus, the corresponding free energy of oligomerization weakly depends on the oligomer size. By contrast, Nutlin-3A has a star-shape and hence can only form stable oligomers when the cluster size is greater than 8. Free energy simulations further confirmed that the free energy of oligomer formation for Nutlin-3A becomes more favorable as the oligomer becomes larger. The aggregation of star-shaped Nutlin-3A results from many-body interactions and hence the free energy of cluster formation is strongly dependent on the size. The findings of this study provide atomistic insights into how molecular shape modulates the aggregation behavior of molecules and may be factored into the design of drugs or nano-particles.

Keeping the ball rolling: fullerene-like molecular clusters.

PubMed

Kong, Xiang-Jian; Long, La-Sheng; Zheng, Zhiping; Huang, Rong-Bin; Zheng, Lan-Sun

2010-02-16

The discovery of fullerenes in 1985 opened a new chapter in the chemistry of highly symmetric molecules. Fullerene-like metal clusters, characterized by (multi)shell-like structures, are one rapidly developing class of molecules that share this shape. In addition to creating aesthetically pleasing molecular structures, the ordered arrangement of metal atoms within such frameworks provides the opportunity to develop materials with properties not readily achieved in corresponding mononuclear or lower-nuclearity complexes. In this Account, we survey the great variety of fullerene-like metal-containing clusters with an emphasis on their synthetic and structural chemistry, a first step in the discussion of this fascinating field of cluster chemistry. We group the compounds of interest into three categories based on the atomic composition of the cluster core: those with formal metal-metal bonding, those characterized by ligand participation, and those supported by polyoxometalate building blocks. The number of clusters in the first group, containing metal-metal bonds, is relatively small. However, because of the unique and complex bonding scenarios observed for some of these species, these metalloid clusters present a number of research questions with significant ramifications. Because these cores contain molecular clusters of precious metals at the nanoscale, they offer an opportunity to study chemical properties at size ranges from the molecular to nanoscale and to gain insights into the electronic structures and properties of nanomaterials of similar chemical compositions. Clusters of the second type, whose core structures are facilitated by ligand participation, could aid in the development of functional materials. Of particular interest are the magnetic clusters containing both transition and lanthanide elements. A series of such heterometallic clusters that we prepared demonstrates diverse magnetic properties including antiferromagnetism, ferrimagnetism, and ferromagnetism. Considering the diversity of their composition, their distinct electronic structures, and the disparate coordination behaviors of the different metal elements, these materials suggest abundant opportunities for designing multifunctional materials with varied structures. The third type of clusters that we discuss are based on polyoxometalates, in particular those containing pentagonal units. However, unlike in fullerene chemistry, which does not allow the use of discrete pentagonal building blocks, the metal oxide-based pentagonal units can be used as fundamental building blocks for constructing various Keplerate structures. These structures also have a variety of functions, including intriguing magnetic properties in some cases. Coupled with different linking groups, such pentagonal units can be used for the assembly of a large number of spherical molecules whose properties can be tuned and optimized. Although this Account focuses on the topological aspects of fullerene-like metal clusters, we hope that this topical review will stimulate more efforts in the exploratory synthesis of new fullerene-like clusters. More importantly, we hope that further study of the bonding interactions and properties of these molecules will lead to the development of new functional materials.

Hybrid MC/QC simulations of water-assisted proton transfer in nucleosides. Guanosine and its analog acyclovir.

PubMed

Markova, Nadezhda; Pejov, Ljupco; Stoyanova, Nina; Enchev, Venelin

2017-05-01

To provide an in-depth insight into the molecular basis of spontaneous tautomerism in DNA and RNA base pairs, a hybrid Monte Carlo (MC)-quantum chemical (QC) methodology is implemented to map two-dimensional potential energy surfaces along the reaction coordinates of solvent-assisted proton transfer processes in guanosine and its analog acyclovir in aqueous solution. The solvent effects were simulated by explicit inclusion of water molecules that model the relevant part of the first hydration shell around the solute. The position of these water molecules was estimated by carrying out a classical Metropolis Monte Carlo simulation of dilute water solutions of the guanosine (Gs) and acyclovir (ACV) and subsequently analyzing solute-solvent intermolecular interactions in the statistically-independent MC-generated configurations. The solvent-assisted proton transfer processes were further investigated using two different ab initio MP2 quantum chemical approaches. In the first one, potential energy surfaces of the 'bare' finite solute-solvent clusters containing Gs/ACV and four water molecules (MP2/6-31+G(d,p) level) were explored, while within the second approach, these clusters were embedded in 'bulk' solvent treated as polarizable continuum (C-PCM/MP2/6-31+G(d,p) level of theory). It was found that in the gas phase and in water solution, the most stable tautomer for guanosine and acyclovir is the 1H-2-amino-6-oxo form followed by the 2-amino-6-(sZ)-hydroxy form. The energy barriers of the water-assisted proton transfer reaction in guanosine and in acyclovir are found to be very similar - 11.74 kcal mol -1 for guanosine and 11.16 kcal mol -1 for acyclovir, and the respective rate constants (k = 1.5 × 10 1 s -1 , guanosine and k = 4.09 × 10 1 s -1 , acyclovir), are sufficiently large to generate the 2-amino-6-(sZ)-hydroxy tautomer. The analysis of the reaction profiles in both compounds shows that the proton transfer processes occur through the asynchronous concerted mechanism.

Al7CX (X=Li-Cs) clusters: Stability and the prospect for cluster materials

NASA Astrophysics Data System (ADS)

Ashman, C.; Khanna, S. N.; Pederson, M. R.; Kortus, J.

2000-12-01

Al7C clusters, recently found to have a high-electron affinity and exceptional stability, are shown to form ionic molecules when combined with alkali-metal atoms. Our studies, based on an ab initio gradient-corrected density-functional scheme, show that Al7CX (X=Li-Cs) clusters have a very low-electron affinity and a high-ionization potential. When combined, the two- and four-atom composite clusters of Al7CLi units leave the Al7C clusters almost intact. Preliminary studies indicate that Al7CLi may be suitable to form cluster-based materials.

Development of non-bonded interaction parameters between graphene and water using particle swarm optimization.

PubMed

Bejagam, Karteek K; Singh, Samrendra; Deshmukh, Sanket A

2018-05-05

New Lennard-Jones parameters have been developed to describe the interactions between atomistic model of graphene, represented by REBO potential, and five commonly used all-atom water models, namely SPC, SPC/E, SPC/Fw, SPC/Fd, and TIP3P/Fs by employing particle swarm optimization (PSO) method. These new parameters were optimized to reproduce the macroscopic contact angle of water on a graphene sheet. The calculated line tension was in the order of 10 -11 J/m for the droplets of all water models. Our molecular dynamics simulations indicate the preferential orientation of water molecules near graphene-water interface with one OH bond pointing toward the graphene surface. Detailed analysis of simulation trajectories reveals the presence of water molecules with ≤∼1, ∼2, and ∼4 hydrogen bonds at the surface of air-water interface, graphene-water interface, and bulk region of the water droplet, respectively. Presence of water molecules with ≤∼1 and ∼2 hydrogen bonds suggest the existence of water clusters of different sizes at these interfaces. The trends observed in the libration, bending, and stretching bands of the vibrational spectra are closely associated with these structural features of water. The inhomogeneity in hydrogen bond network of water at the air-water and graphene-water interface is manifested by broadening of the peaks in the libration band for water present at these interfaces. The stretching band for the molecules in water droplet shows a blue shift as compared to the pure bulk water, which conjecture the presence of weaker hydrogen bond network in a droplet. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

The L1-type cell adhesion molecule Neuroglian is necessary for maintenance of sensory axon advance in the Drosophila embryo.

PubMed

Martin, Veronica; Mrkusich, Eli; Steinel, Martin C; Rice, Jason; Merritt, David J; Whitington, Paul M

2008-04-08

Cell adhesion molecules have long been implicated in the regulation of axon growth, but the precise cellular roles played by individual cell adhesion molecules and the molecular basis for their action are still not well understood. We have used the sensory system of the Drosophila embryo to shed light on the mechanism by which the L1-type cell adhesion molecule Neuroglian regulates axon growth. We have found a highly penetrant sensory axon stalling phenotype in neuroglian mutant embryos. Axons stalled at a variety of positions along their normal trajectory, but most commonly in the periphery some distance along the peripheral nerve. All lateral and dorsal cluster sensory neurons examined, except for the dorsal cluster neuron dbd, showed stalling. Sensory axons were never seen to project along inappropriate pathways in neuroglian mutants and stalled axons showed normal patterns of fasciculation within nerves. The growth cones of stalled axons possessed a simple morphology, similar to their appearance in wild-type embryos when advancing along nerves. Driving expression of the wild-type form of Neuroglian in sensory neurons alone rescued the neuroglian mutant phenotype of both pioneering and follower neurons. A partial rescue was achieved by expressing the Neuroglian extracellular domain. Over/mis-expression of Neuroglian in all neurons, oenocytes or trachea had no apparent effect on sensory axon growth. We conclude that Neuroglian is necessary to maintain axon advance along axonal substrates, but is not required for initiation of axon outgrowth, axon fasciculation or recognition of correct growth substrates. Expression of Neuroglian in sensory neurons alone is sufficient to promote axon advance and the intracellular region of the molecule is largely dispensable for this function. It is unlikely, therefore, that Nrg acts as a molecular 'clutch' to couple adhesion of F-actin within the growth cone to the extracellular substrate. Rather, we suggest that Neuroglian mediates sensory axon advance by promoting adhesion of the surface of the growth cone to its substrate. Our finding that stalling of a pioneer sensory neuron is rescued by driving Neuroglian in sensory neurons alone may suggest that Neuroglian can act in a heterophilic fashion.

The L1-type cell adhesion molecule Neuroglian is necessary for maintenance of sensory axon advance in the Drosophila embryo

PubMed Central

Martin, Veronica; Mrkusich, Eli; Steinel, Martin C; Rice, Jason; Merritt, David J; Whitington, Paul M

2008-01-01

Background Cell adhesion molecules have long been implicated in the regulation of axon growth, but the precise cellular roles played by individual cell adhesion molecules and the molecular basis for their action are still not well understood. We have used the sensory system of the Drosophila embryo to shed light on the mechanism by which the L1-type cell adhesion molecule Neuroglian regulates axon growth. Results We have found a highly penetrant sensory axon stalling phenotype in neuroglian mutant embryos. Axons stalled at a variety of positions along their normal trajectory, but most commonly in the periphery some distance along the peripheral nerve. All lateral and dorsal cluster sensory neurons examined, except for the dorsal cluster neuron dbd, showed stalling. Sensory axons were never seen to project along inappropriate pathways in neuroglian mutants and stalled axons showed normal patterns of fasciculation within nerves. The growth cones of stalled axons possessed a simple morphology, similar to their appearance in wild-type embryos when advancing along nerves. Driving expression of the wild-type form of Neuroglian in sensory neurons alone rescued the neuroglian mutant phenotype of both pioneering and follower neurons. A partial rescue was achieved by expressing the Neuroglian extracellular domain. Over/mis-expression of Neuroglian in all neurons, oenocytes or trachea had no apparent effect on sensory axon growth. Conclusion We conclude that Neuroglian is necessary to maintain axon advance along axonal substrates, but is not required for initiation of axon outgrowth, axon fasciculation or recognition of correct growth substrates. Expression of Neuroglian in sensory neurons alone is sufficient to promote axon advance and the intracellular region of the molecule is largely dispensable for this function. It is unlikely, therefore, that Nrg acts as a molecular 'clutch' to couple adhesion of F-actin within the growth cone to the extracellular substrate. Rather, we suggest that Neuroglian mediates sensory axon advance by promoting adhesion of the surface of the growth cone to its substrate. Our finding that stalling of a pioneer sensory neuron is rescued by driving Neuroglian in sensory neurons alone may suggest that Neuroglian can act in a heterophilic fashion. PMID:18397531

Light controllable catalytic activity of Au clusters decorated with photochromic molecules.

PubMed

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

2018-06-15

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 Au 8 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-Au 8 ) 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-Au 8 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.

Light controllable catalytic activity of Au clusters decorated with photochromic molecules

NASA Astrophysics Data System (ADS)

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.

Spontaneously amplified homochiral organic-inorganic nano-helix complexes via self-proliferation.

PubMed

Zhai, Halei; Quan, Yan; Li, Li; Liu, Xiang-Yang; Xu, Xurong; Tang, Ruikang

2013-04-07

Most spiral coiled biomaterials in nature, such as gastropod shells, are homochiral, and the favoured chiral feature can be precisely inherited. This inspired us that selected material structures, including chirality, could be specifically replicated into the self-similar populations; however, a physicochemical understanding of the material-based heritage is unknown. We study the homochirality by using calcium phosphate mineralization in the presence of racemic amphiphilic molecules and biological protein. The organic-inorganic hybrid materials with spiral coiling characteristics are produced at the nanoscale. The resulted helixes are chiral with the left- and right-handed characteristics, which are agglomerated hierarchically to from clusters and networks. It is interesting that each cluster or network is homochiral so that the enantiomorphs can be separated readily. Actually, each homochiral architecture is evolved from an original chiral helix, demonstrating the heritage of the matrix chirality during the material proliferation under a racemic condition. By using the Ginzburg-Landaue expression we find that the chiral recognition in the organic-inorganic hybrid formation may be determined by a spontaneous chiral separation and immobilization of asymmetric amphiphilic molecules on the mineral surface, which transferred the structural information from the mother matrix to the descendants by an energetic control. This study shows how biomolecules guide the selective amplification of chiral materials via spontaneous self-replication. Such a strategy can be applied generally in the design and production of artificial materials with self-similar structure characteristics.

Basis set limit and systematic errors in local-orbital based all-electron DFT

NASA Astrophysics Data System (ADS)

Blum, Volker; Behler, Jörg; Gehrke, Ralf; Reuter, Karsten; Scheffler, Matthias

2006-03-01

With the advent of efficient integration schemes,^1,2 numeric atom-centered orbitals (NAO's) are an attractive basis choice in practical density functional theory (DFT) calculations of nanostructured systems (surfaces, clusters, molecules). Though all-electron, the efficiency of practical implementations promises to be on par with the best plane-wave pseudopotential codes, while having a noticeably higher accuracy if required: Minimal-sized effective tight-binding like calculations and chemically accurate all-electron calculations are both possible within the same framework; non-periodic and periodic systems can be treated on equal footing; and the localized nature of the basis allows in principle for O(N)-like scaling. However, converging an observable with respect to the basis set is less straightforward than with competing systematic basis choices (e.g., plane waves). We here investigate the basis set limit of optimized NAO basis sets in all-electron calculations, using as examples small molecules and clusters (N2, Cu2, Cu4, Cu10). meV-level total energy convergence is possible using <=50 basis functions per atom in all cases. We also find a clear correlation between the errors which arise from underconverged basis sets, and the system geometry (interatomic distance). ^1 B. Delley, J. Chem. Phys. 92, 508 (1990), ^2 J.M. Soler et al., J. Phys.: Condens. Matter 14, 2745 (2002).

Distributions of methyl group rotational barriers in polycrystalline organic solids

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

Beckmann, Peter A., E-mail: pbeckman@brynmawr.edu, E-mail: wangxianlong@uestc.edu.cn; Conn, Kathleen G.; Division of Education and Human Services, Neumann University, One Neumann Drive, Aston, Pennsylvania 19014-1298

We bring together solid state {sup 1}H spin-lattice relaxation rate measurements, scanning electron microscopy, single crystal X-ray diffraction, and electronic structure calculations for two methyl substituted organic compounds to investigate methyl group (CH{sub 3}) rotational dynamics in the solid state. Methyl group rotational barrier heights are computed using electronic structure calculations, both in isolated molecules and in molecular clusters mimicking a perfect single crystal environment. The calculations are performed on suitable clusters built from the X-ray diffraction studies. These calculations allow for an estimate of the intramolecular and the intermolecular contributions to the barrier heights. The {sup 1}H relaxation measurements,more » on the other hand, are performed with polycrystalline samples which have been investigated with scanning electron microscopy. The {sup 1}H relaxation measurements are best fitted with a distribution of activation energies for methyl group rotation and we propose, based on the scanning electron microscopy images, that this distribution arises from molecules near crystallite surfaces or near other crystal imperfections (vacancies, dislocations, etc.). An activation energy characterizing this distribution is compared with a barrier height determined from the electronic structure calculations and a consistent model for methyl group rotation is developed. The compounds are 1,6-dimethylphenanthrene and 1,8-dimethylphenanthrene and the methyl group barriers being discussed and compared are in the 2–12 kJ mol{sup −1} range.« less

Predicting the points of interaction of small molecules in the NF-κB pathway

PubMed Central

2011-01-01

Background The similarity property principle has been used extensively in drug discovery to identify small compounds that interact with specific drug targets. Here we show it can be applied to identify the interactions of small molecules within the NF-κB signalling pathway. Results Clusters that contain compounds with a predominant interaction within the pathway were created, which were then used to predict the interaction of compounds not included in the clustering analysis. Conclusions The technique successfully predicted the points of interactions of compounds that are known to interact with the NF-κB pathway. The method was also shown to be successful when compounds for which the interaction points were unknown were included in the clustering analysis. PMID:21342508

Structure formation of lipid membranes: Membrane self-assembly and vesicle opening-up to octopus-like micelles

NASA Astrophysics Data System (ADS)

Noguchi, Hiroshi

2013-02-01

We briefly review our recent studies on self-assembly and vesicle rupture of lipid membranes using coarse-grained molecular simulations. For single component membranes, lipid molecules self-assemble from random gas states to vesicles via disk-shaped clusters. Clusters aggregate into larger clusters, and subsequently the large disks close into vesicles. The size of vesicles are determined by kinetics than by thermodynamics. When a vesicle composed of lipid and detergent types of molecules is ruptured, a disk-shaped micelle called bicelle can be formed. When both surfactants have negligibly low critical micelle concentration, it is found that bicelles connected with worm-like micelles are also formed depending on the surfactant ratio and spontaneous curvature of the membrane monolayer.

On the applicability of one- and many-electron quantum chemistry models for hydrated electron clusters

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

Turi, László, E-mail: turi@chem.elte.hu

2016-04-21

We evaluate the applicability of a hierarchy of quantum models in characterizing the binding energy of excess electrons to water clusters. In particular, we calculate the vertical detachment energy of an excess electron from water cluster anions with methods that include one-electron pseudopotential calculations, density functional theory (DFT) based calculations, and ab initio quantum chemistry using MP2 and eom-EA-CCSD levels of theory. The examined clusters range from the smallest cluster size (n = 2) up to nearly nanosize clusters with n = 1000 molecules. The examined cluster configurations are extracted from mixed quantum-classical molecular dynamics trajectories of cluster anions withmore » n = 1000 water molecules using two different one-electron pseudopotenial models. We find that while MP2 calculations with large diffuse basis set provide a reasonable description for the hydrated electron system, DFT methods should be used with precaution and only after careful benchmarking. Strictly tested one-electron psudopotentials can still be considered as reasonable alternatives to DFT methods, especially in large systems. The results of quantum chemistry calculations performed on configurations, that represent possible excess electron binding motifs in the clusters, appear to be consistent with the results using a cavity structure preferring one-electron pseudopotential for the hydrated electron, while they are in sharp disagreement with the structural predictions of a non-cavity model.« less