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1

Algorithm for Reconstruction of 3D Molecular Structure from Diffraction Patterns of Laser-Aligned Molecules  

NASA Astrophysics Data System (ADS)

Ultrafast electron diffraction from laser-aligned gas molecules is a promising method for the determination of 3D molecular structures. Reconstruction algorithms for diffraction patterns of perfectly aligned molecules have been widely studied theoretically. However, under experimental conditions only partial alignment can be achieved and the existing algorithms do not perform well when the alignment is not perfect. We develop a method to reconstruct the 3D structure of molecules with cylindrical symmetry from electron diffraction patterns of partially-aligned molecules. The evolutionary algorithm assumes a known angular distribution, which can be calculated numerically using existing theory for laser-alignment and verified by comparison with the data. Selecting CF3I as the cylindrically symmetric molecule, diffraction patterns from multiple alignment angles are used to reconstruct a single diffraction pattern corresponding to perfect alignment. The molecular structure can then be recovered from this pattern with no prior structural information required. Our results are in good agreement with previous models of CF3I structure.

Yang, Jie; Hensley, Christopher; Centurion, Martin

2012-06-01

2

Molecular structure determination from x-ray scattering patterns of laser-aligned symmetric-top molecules  

Microsoft Academic Search

We investigate the molecular structure information contained in the x-ray diffraction patterns of an ensemble of rigid CF3Br molecules aligned by an intense laser pulse at finite rotational temperature. The diffraction patterns are calculated at an x-ray photon energy of 20 keV to probe molecular structure at angstrom-scale resolution. We find that a structural reconstruction algorithm based on iterative phase

P. J. Ho; D. Starodub; D. K. Saldin; V. L. Shneerson; A. Ourmazd; R. Santra

2009-01-01

3

Molecular structure determination from x-ray scattering patterns of laser-aligned symmetric-top molecules  

SciTech Connect

We investigate the molecular structure information contained in the x-ray diffraction patterns of an ensemble of rigid CF{sub 3}Br molecules aligned by an intense laser pulse at finite rotational temperature. The diffraction patterns are calculated at an x-ray photon energy of 20 keV to probe molecular structure at angstrom-scale resolution. We find that a structural reconstruction algorithm based on iterative phase retrieval fails to extract a reliable structure. However, the high atomic number of Br compared with C or F allows each diffraction pattern to be treated as a hologram. Using this approach, the azimuthal projection of the molecular electron density about the alignment axis may be retrieved.

Ho, P. J. [Argonne National Laboratory, Argonne, Illinois 60439 (United States); Starodub, D. [Department of Physics, Arizona State University, Tempe, Arizona 85287 (United States); Saldin, D. K.; Shneerson, V. L.; Ourmazd, A. [Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53201 (United States); Santra, R. [Argonne National Laboratory, Argonne, Illinois 60439 (United States); Department of Physics, University of Chicago, Chicago, Illinois 60637 (United States)

2009-10-07

4

Molecular structure determination from x-ray scattering patterns of laser-aligned symmetric-top molecules.  

SciTech Connect

We investigate the molecular structure information contained in the x-ray diffraction patterns of an ensemble of rigid CF{sub 3}Br molecules aligned by an intense laser pulse at finite rotational temperature. The diffraction patterns are calculated at an x-ray photon energy of 20 keV to probe molecular structure at angstrom-scale resolution. We find that a structural reconstruction algorithm based on iterative phase retrieval fails to extract a reliable structure. However, the high atomic number of Br compared with C or F allows each diffraction pattern to be treated as a hologram. Using this approach, the azimuthal projection of the molecular electron density about the alignment axis may be retrieved.

Ho, P. J.; Starodub, D.; Saldin, D. K.; Shneerson, V. L.; Ourmazd, A.; Santra, R.; Arizona State Univ.; Univ. of Wisconsin at Milwaukee; Univ. of Chicago

2009-10-07

5

Molecular structure determination from x-ray scattering patterns of laser-aligned symmetric-top molecules  

NASA Astrophysics Data System (ADS)

We investigate the molecular structure information contained in the x-ray diffraction patterns of an ensemble of rigid CF3Br molecules aligned by an intense laser pulse at finite rotational temperature. The diffraction patterns are calculated at an x-ray photon energy of 20 keV to probe molecular structure at angstrom-scale resolution. We find that a structural reconstruction algorithm based on iterative phase retrieval fails to extract a reliable structure. However, the high atomic number of Br compared with C or F allows each diffraction pattern to be treated as a hologram. Using this approach, the azimuthal projection of the molecular electron density about the alignment axis may be retrieved.

Ho, P. J.; Starodub, D.; Saldin, D. K.; Shneerson, V. L.; Ourmazd, A.; Santra, R.

2009-10-01

6

Molecular structure determination from x-ray scattering patterns of laser-aligned symmetric-top molecules.  

PubMed

We investigate the molecular structure information contained in the x-ray diffraction patterns of an ensemble of rigid CF(3)Br molecules aligned by an intense laser pulse at finite rotational temperature. The diffraction patterns are calculated at an x-ray photon energy of 20 keV to probe molecular structure at angstrom-scale resolution. We find that a structural reconstruction algorithm based on iterative phase retrieval fails to extract a reliable structure. However, the high atomic number of Br compared with C or F allows each diffraction pattern to be treated as a hologram. Using this approach, the azimuthal projection of the molecular electron density about the alignment axis may be retrieved. PMID:19814536

Ho, P J; Starodub, D; Saldin, D K; Shneerson, V L; Ourmazd, A; Santra, R

2009-10-01

7

Computational study of decomposition mechanisms and thermodynamic properties of molecular-type cracking patterns for the highly energetic molecule GZT.  

PubMed

This study uses the Gaussian 03 program and density functional theory B3LYP with three basis set methods-[B3LYP/6-311+G(d,p), B3LYP/6-31+G(2d,p), and B3LYP/6-31G(d,p)]-to model the highly energetic ionic compound diguanidinium 5,5'-azotetrazolate (GZT) to research its decomposition mechanisms and thermodynamic properties. Molecular-type cracking patterns are proposed, which were initiated by heterocyclic ring opening, sequential cracking of the two five-membered rings of GZT, and simultaneous release of N2 molecules; whereas proton transfer, bond-breaking, and atomic rearrangements were performed subsequently. Finally, 15 reaction paths and five transition states were obtained. All possible decomposition species and transition states, including intermediates and products, were identified, and their corresponding enthalpy and Gibbs free energy values were obtained. The results revealed that (1) the maximum activation energy required is 187.8 kJ mol(-1), and the enthalpy change (?H) and Gibbs free-energy change (?G) of the net reaction are -525.1 kJ mol(-1) and -935.6 kJ mol(-1), respectively; (2) GZT can release large amounts of energy, the main contribution being from the disintegration of the 5,5'-azotetrazolate anion (ZT(2-)) skeleton (?H = -598.3 kJ mol(-1)); and (3) the final products contained major amounts of N2 gas, but remaining gas molecules such as HCN and NH3 were obtained, which are in agreement with experimental results. The detailed decomposition simulation results demonstrated the feasibility of this method to calculate the energies of the thermodynamic reactions for the highly energetic GZT and predict the most feasible pathways and the final products. PMID:23780346

Cheng, Sou-Ro; Cheng, Ken-Fa; Liu, Min-Hsien; Hong, Yaw-Shun; Chen, Cheng

2013-06-19

8

Damage Associated Molecular Pattern Molecule-Induced microRNAs (DAMPmiRs) in Human Peripheral Blood Mononuclear Cells  

PubMed Central

Endogenous damage associated molecular pattern molecules (DAMPs) released from necrotic, damaged or stressed cells are associated with an inflammatory response. Whether the microRNA (miR) expression signature of this response is different from that of a pathogen associated molecular pattern (PAMP)-stimulated inflammatory response is unknown. We report here that miR-34c and miR-214 are significantly expressed in fresh human peripheral blood mononuclear cells (PBMCs) exposed to DAMP-containing freeze-thaw lysates, or to conditioned media from serum-starved and glucose-deprived cells (p<6×10?4 and p<3.7×10?3), respectively. Interestingly, only miR-34c expression was differentially expressed in PBMCs exposed to freeze-thaw lysates or conditioned media from wildtype High Mobility Group B1 (HMGB1+/+) mouse embryonic fibroblast (MEF) cells, when compared to cultures exposed to lysates or conditioned media from HMGB1?/? MEFs. miR-155 expression in these cultures was negligible, but was significantly expressed in PBMCs stimulated with Lipopolysaccahride (LPS) or most other Toll-like receptor (TLR) ligands, making it the prototypic “PAMPmiR”. Exposure to a damaged human colorectal carcinoma cell line lysate (HCT116) similarly resulted in increased miR-34c and miR-214 levels. When PBMCs were pre-transfected with anti-miR-34c and then exposed to lysate, expression levels of IKK? mRNA, a putative target of miR-34c, increased, while protein levels of IKK? in cultures transfected with a pre-miR-34c were abrogated. Levels of miR-34c expression (as well as pro-inflammatory cytokines, IL-1? and TNF?) decreased when PBMC cultures were briefly pre-incubated with the K+ channel (inflammasome) inhibitor, glybenclamide, suggesting that inflammasome activation is upstream of miR-34c expression in response to DAMPs. Our findings demonstrate that a specific microRNA expression signature is associated with the inflammatory response to damaged/injured cells and carries implications for many acute and chronic inflammatory disorders.

Unlu, Sebnem; Tang, Siuwah; Wang, E. na; Martinez, Ivan; Tang, Daolin; Bianchi, Marco E.; Zeh, Herbert J.; Lotze, Michael T.

2012-01-01

9

IgG antibodies from dourine infected horses identify a distinctive Trypanosoma equiperdum antigenic pattern of low molecular weight molecules.  

PubMed

Diagnosis and control of dourine is strongly based on serological evidence, but knowledge of the humoral response of horses during infection is limited. In this study we developed a chemiluminescent immunoblotting (cIB) assay to characterise the Trypanosoma equiperdum antigen pattern recognised by IgGs from naturally or experimentally dourine-infected horses and analyse the kinetics of IgG humoral response following the infection. One compounding factor is that sera from uninfected animals often cross-react with T. equiperdum antigens. Development of the cIB assay was based on the hypothesis that serum IgGs from healthy and infected animals recognise different T. equiperdum antigen patterns. We used sera from 8 naturally infected horses which had recovered from Italian outbreaks and 2 experimentally infected mares. In addition, sera from 10 healthy control animals, eight of which were CFT positive but IFA negative for dourine, were collected from disease free regions. Sera were compared by the complement fixation test (CFT), indirect immune fluorescence (IFA) and the cIB assay. cIB analysis revealed that IgGs from infected horses, in contrast to IgGs from healthy horses, specifically recognise a T. equiperdum antigenic profile with low molecular weight bands ranging between 16 and 35 kDa. A time course experiment indicated that IgGs specific for the 16-35 kDa parasite protein fraction appear 17 days post-infection. The cIB assay confirmed all ten infected animals as positive and all controls as negative. This study demonstrated that analysis of IgGs by cIB can provide clear confirmation of trypanosome infection in horses, suggesting that this technique can be applied as a confirmatory serological test for dourine infection. PMID:23218944

Luciani, M; Di Pancrazio, C; Di Febo, T; Tittarelli, M; Podaliri Vulpiani, M; Puglielli, M O; Naessens, J; Sacchini, F

2012-11-14

10

Micro-patterning of multiple organic molecules by laser implantation  

Microsoft Academic Search

Micrometer pixelated arrays comprised of different functional organic molecules were formed on a polymer film using a laser implantation and transfer dry processing technique. The spatial distribution of the implanted organic molecules and the extended pattern that they formed could be controlled with high resolution as determined using fluorescence microscopy. The individual molecular implant pixels had a diameter of less

M. Goto; J. Hobley; T. Oishi; A. Kasahara; M. Tosa; K. Yoshihara; M. Kishimoto; H. Fukumura

2004-01-01

11

Sequence-Specific Molecular Lithography on Single DNA Molecules  

Microsoft Academic Search

Recent advances in the realization of individual molecular-scale electronic devices emphasize the need for novel tools and concepts capable of assembling such devices into large-scale functional circuits. We demonstrated sequence-specific molecular lithography on substrate DNA molecules by harnessing homologous recombination by RecA protein. In a sequence-specific manner, we patterned the coating of DNA with metal, localized labeled molecular objects and

Kinneret Keren; Michael Krueger; Rachel Gilad; Gdalyahu Ben-Yoseph; Uri Sivan; Erez Braun

2002-01-01

12

Molecular spintronics using single-molecule magnets  

Microsoft Academic Search

A revolution in electronics is in view, with the contemporary evolution of the two novel disciplines of spintronics and molecular electronics. A fundamental link between these two fields can be established using molecular magnetic materials and, in particular, single-molecule magnets. Here, we review the first progress in the resulting field, molecular spintronics, which will enable the manipulation of spin and

Lapo Bogani; Wolfgang Wernsdorfer

2008-01-01

13

Structure factor and rheology of chain molecules from molecular dynamics  

NASA Astrophysics Data System (ADS)

Equilibrium and non-equilibrium molecular dynamics were performed to determine the relationship between the static structure factor, the molecular conformation, and the rheological properties of chain molecules. A spring-monomer model with Finitely Extensible Nonlinear Elastic and Lennard-Jones force field potentials was used to describe chain molecules. The equations of motion were solved for shear flow with SLLOD equations of motion integrated with Verlet's algorithm. A multiple time scale algorithm extended to non-equilibrium situations was used as the integration method. Concentric circular patterns in the structure factor were obtained, indicating an isotropic Newtonian behavior. Under simple shear flow, some peaks in the structure factor were emerged corresponding to an anisotropic pattern as chains aligned along the flow direction. Pure chain molecules and chain molecules in solution displayed shear-thinning regions. Power-law and Carreau-Yasuda models were used to adjust the generated data. Results are in qualitative agreement with rheological and light scattering experiments.

Castrejón-González, Omar; Castillo-Tejas, Jorge; Manero, Octavio; Alvarado, Juan F. J.

2013-05-01

14

Automated molecule editing in molecular design.  

PubMed

The ability to modify chemical structures in an automated and controlled manner is useful in molecular design. This Perspective introduces the MUDO molecule editor and shows how automated molecule editing can be used to standardize structures, enumerate tautomeric and ionization states, identify matched molecular pairs. Unlike its predecessor Leatherface, MUDO can also process 3D structures and this capability can be used to link non-covalently docked ligands to proteins. PMID:24002455

Kenny, Peter W; Montanari, Carlos A; Prokopczyk, Igor M; Sala, Fernanda A; Sartori, Geraldo Rodrigues

2013-09-04

15

Bringing Molecules Back into Molecular Evolution  

PubMed Central

Much molecular-evolution research is concerned with sequence analysis. Yet these sequences represent real, three-dimensional molecules with complex structure and function. Here I highlight a growing trend in the field to incorporate molecular structure and function into computational molecular-evolution work. I consider three focus areas: reconstruction and analysis of past evolutionary events, such as phylogenetic inference or methods to infer selection pressures; development of toy models and simulations to identify fundamental principles of molecular evolution; and atom-level, highly realistic computational modeling of molecular structure and function aimed at making predictions about possible future evolutionary events.

Wilke, Claus O.

2012-01-01

16

Molecular-beam spectroscopy of interhalogen molecules  

SciTech Connect

A molecular-beam electric-resonance spectrometer employing a supersonic nozzle source has been used to obtain hyperfine spectra of /sup 79/Br/sup 35/Cl. Analyses of these spectra and of microwave spectra published by other authors have yielded new values for the electric dipole moment and for the nuclear quadrupole coupling constants in this molecule. The new constants are significantly different from the currently accepted values. Van der Waals clusters containing chlorine monofluoride have been studied under various expansion conditions by the molecular-beam electric-deflection method. The structural possibilities indicated by the results are discussed, and cluster geometries are proposed.

Sherrow, S.A.

1983-08-01

17

Dynamic spiral patterns in Langmuir monolayers of chiral molecules  

NASA Astrophysics Data System (ADS)

Experiments with Langmuir monolayers of chiral molecules on a water surface report a collective propeller-like precession of the molecules due to the evaporation of water [1]. If the molecular orientation is pinned along an edge, the precession leads to a series of stripes along the edge. This pattern formation has been explained by a dynamic equation due to the Lehmann effect [2]. Here, we consider how the patterns change if the monolayer contains vortices, topological defects which pin the molecular orientation. We model an annular ring with a single vortex at its center, and show that the director field forms a spiral centered at the defect, which reverses handedness between the inner and outer boundaries. We also simulate a system with one vortex and one anti-vortex on a lattice, and find that the defects form spirals with opposite handedness. These analytic and computational results are in good agreement with preliminary experiments [3]. [1] Y. Tabe, H. Yokoyama, Nat. Mater. 2, 806 (2003). [2] D. Svensek, H. Pleiner, H. R. Brand, Phys. Rev. Lett. 96, 140601 (2006). [3] K. A. Suresh, private communication.

Lopatina, Lena; Selinger, Jonathan V.

2007-03-01

18

Assembling molecular electronic junctions one molecule at a time.  

PubMed

Diffusion of metal atoms onto a molecular monolayer attached to a conducting surface permits electronic contact to the molecules with minimal heat transfer or structural disturbance. Surface-mediated metal deposition (SDMD) involves contact between "cold" diffusing metal atoms and molecules, due to shielding of the molecules from direct exposure to metal vapor. Measurement of the current through the molecular layer during metal diffusion permits observation of molecular conductance for junctions containing as few as one molecule. Discrete conductance steps were observed for 1-10 molecules within a monolayer during a single deposition run, corresponding to "recruitment" of additional molecules as the contact area between the diffusing Au layer and molecules increases. For alkane monolayers, the molecular conductance measured with SDMD exhibited an exponential dependence on molecular length with a decay constant (?) of 0.90 per CH(2) group, comparable to that observed by other techniques. Molecular conductance values were determined for three azobenzene molecules, and correlated with the offset between the molecular HOMO and the contact Fermi level, as expected for hole-mediated tunneling. Current-voltage curves were obtained during metal deposition showed no change in shape for junctions containing 1, 2, and 10 molecules, implying minimal intermolecular interactions as single molecule devices transitioned into several molecules devices. SDMD represents a "soft" metal deposition method capable of providing single molecule conductance values, then providing quantitative comparisons to molecular junctions containing 10(6) to 10(10) molecules. PMID:21995487

Bonifas, Andrew P; McCreery, Richard L

2011-10-18

19

Axon Guidance Molecules in Vascular Patterning  

PubMed Central

Endothelial cells (ECs) form extensive, highly branched and hierarchically organized tubular networks in vertebrates to ensure the proper distribution of molecular and cellular cargo in the vertebrate body. The growth of this vascular system during development, tissue repair or in disease conditions involves the sprouting, migration and proliferation of endothelial cells in a process termed angiogenesis. Surprisingly, specialized ECs, so-called tip cells, which lead and guide endothelial sprouts, share many feature with another guidance structure, the axonal growth cone. Tip cells are motile, invasive and extend numerous filopodial protrusions sensing growth factors, extracellular matrix and other attractive or repulsive cues in their tissue environment. Axonal growth cones and endothelial tip cells also respond to signals belonging to the same molecular families, such as Slits and Roundabouts, Netrins and UNC5 receptors, Semaphorins, Plexins and Neuropilins, and Eph receptors and ephrin ligands. Here we summarize fundamental principles of angiogenic growth, the selection and function of tip cells and the underlying regulation by guidance cues, the Notch pathway and vascular endothelial growth factor signaling.

Adams, Ralf H.; Eichmann, Anne

2010-01-01

20

Single DNA Molecule Patterning for High-Throughput Epigenetic Mapping  

PubMed Central

We present a method for profiling the 5-methyl cytosine distribution on single DNA molecules. Our method combines soft-lithography and molecular elongation to form ordered arrays of more than 250,000 individual DNA molecules immobilized on a solid substrate. The methylation state of the DNA is detected and mapped by binding of fluorescently labeled methyl-CpG binding domain peptides to the elongated dsDNA molecules and imaging of their distribution. The stretched molecules are fixed in their extended configuration by adsorption onto the substrate so analysis can be performed with high spatial resolution and signal averaging. We further prove this technique allows imaging of DNA molecules with different methylation states.

Cerf, Aline; Cipriany, Benjamin R.; Benitez, Jaime J.; Craighead, Harold G.

2013-01-01

21

Molecular wring resonances in chain molecules.  

PubMed

It is shown that the eigenfrequency of collective twist excitations in chain molecules can be in the megahertz and gigahertz range. Accordingly, resonance states can be obtained at specific frequencies, and phenomena that involve structural properties can take place. Chain molecules can alter their conformation and their ability to function, and a breaking of the chain can result. It is suggested that this phenomenon forms the basis for effects caused by the interaction of microwaves and biomolecules, e.g., microwave assisted hydrolysis of chain molecules. PMID:9084871

Bohr, H; Brunak, S; Bohr, J

1997-01-01

22

Conformational flexibility and hydrogen-bonding patterns of the neotame molecule in its various solid forms.  

PubMed

The conformational flexibility and the molecular packing patterns of the neotame molecule in its various crystal forms, including neotame monohydrate, methanol solvate, ethanol solvate, benzene solvate, and anhydrate polymorph G, are analyzed in this work. The Cerius2 molecular modeling program with the Dreiding 2.21 force field was employed to calculate the most stable conformations of neotame molecules in the gaseous state and to analyze the conformations of the neotame molecule in its various crystal forms. Using graph set analysis, the hydrogen bond patterns of these crystal forms were compared. The neotame molecule takes different conformations in its crystal forms and in the free gaseous state. Cerius2 found 10 conformers with lower conformational energies than those in the actual crystal structures, which represent an energetic compromise. The relatively large differences between the energies of the conformers indicate the necessity for rewriting or customizing the force field for neotame. The hydrogen bonding patterns of the neotame methanol and ethanol solvates are identical, but different from those of the other three forms, which also differ from each other. The neotame molecule in its various crystal forms takes different conformations that differ from those in the gaseous state because of the influence of crystal packing. The intramolecular ring, S5, is present in all the crystal forms. The following hydrogen bonding patterns occur in some of the crystal forms: diad, D; intramolecular rings, S(6) and S(7); chains, C(5) and C(6); and an intermolecular ring, R2(2)(12). PMID:12210051

Dong, Zedong; Munson, Eric J; Schroeder, Steve A; Prakash, Indra; Grant, David J W

2002-09-01

23

Efficient unfolding pattern recognition in single molecule force spectroscopy data  

PubMed Central

Background Single-molecule force spectroscopy (SMFS) is a technique that measures the force necessary to unfold a protein. SMFS experiments generate Force-Distance (F-D) curves. A statistical analysis of a set of F-D curves reveals different unfolding pathways. Information on protein structure, conformation, functional states, and inter- and intra-molecular interactions can be derived. Results In the present work, we propose a pattern recognition algorithm and apply our algorithm to datasets from SMFS experiments on the membrane protein bacterioRhodopsin (bR). We discuss the unfolding pathways found in bR, which are characterised by main peaks and side peaks. A main peak is the result of the pairwise unfolding of the transmembrane helices. In contrast, a side peak is an unfolding event in the alpha-helix or other secondary structural element. The algorithm is capable of detecting side peaks along with main peaks. Therefore, we can detect the individual unfolding pathway as the sequence of events labeled with their occurrences and co-occurrences special to bR's unfolding pathway. We find that side peaks do not co-occur with one another in curves as frequently as main peaks do, which may imply a synergistic effect occurring between helices. While main peaks co-occur as pairs in at least 50% of curves, the side peaks co-occur with one another in less than 10% of curves. Moreover, the algorithm runtime scales well as the dataset size increases. Conclusions Our algorithm satisfies the requirements of an automated methodology that combines high accuracy with efficiency in analyzing SMFS datasets. The algorithm tackles the force spectroscopy analysis bottleneck leading to more consistent and reproducible results.

2011-01-01

24

Ultrafast dynamics in isolated molecules and molecular clusters  

Microsoft Academic Search

During the past decade the understanding of photo-induced ultrafast dynamics in molecular systems has improved at an unforeseen speed and a wealth of detailed insight into the fundamental processes has been obtained. This review summarizes our present knowledge on ultrafast dynamics in isolated molecules and molecular clusters evolving after excitation with femtosecond pulses as studied by pump-probe analysis in real

I. V. Hertel; W. Radloff

2006-01-01

25

Regular and anomalous torsional splitting patterns: a trend in ethane-like molecules and general perspectives  

NASA Astrophysics Data System (ADS)

It is shown that torsional Coriolis coupling can alter the torsional splittings in molecules with hindered internal rotation. Splitting patterns that would occur in the absence of any vibrational contribution to the torsional angular momentum, with reference to a molecular axis system (IAM), are called regular. It is shown that different sets of vibrational coordinates, corresponding to vibrational states with different splitting patterns, can be defined for modes normal to the internal rotation axis. The forms of normal coordinates appropriate to basis vibrational states with regular and inverted splitting patterns are identified. It is found that in normal coordinates appropriate to vibrational states with regular torsional splitting patterns, the relative orientation of the displacements of pairs of atoms belonging to different molecular moieties is independent of the internal rotation angle, and relative displacements normal to the internal rotation axis can be cis or trans at any conformation. On the contrary, in normal coordinates appropriate to vibrational states with inverted torsional splitting patterns the relative orientation of such displacements changes by ?(cis-trans interchange) upon half the internal rotation converting two neighbor equivalent conformations (as in a staggered-eclipsed conformational conversion). The formation of the actual torsional splitting patterns in degenerate vibrational states of CH3CH3-type molecules depends on the joint effect of torsional Coriolis and head-tail coupling. The torsional Coriolis operator can tune pairs of levels to resonance for the action of typical head-tail coupling operators (torsion-dependent vibrational operators), depending on the values of the torsional Coriolis coefficients, generating vibrational states with either regular or inverted torsional splitting patterns and affecting the splitting magnitude. It is shown that operators with a sin3?-type torsional dependence favor the formation of inverted splitting patterns. In less symmetric molecules torsional Coriolis coupling affects the torsional splitting patterns by the same mechanism as in CH3CH3-type molecules, but the torsion-dependent operators are different and their action is expected to be less effective. Typical anomalous perpendicular splitting patterns can be predicted for non-degenerate modes localized in a single molecular moiety, normal or with a component normal to the internal rotation axis, having fixed orientation in that moiety (as the C=O or C-H stretchings of acetaldehyde). Adopting a barrier-hindered torsional basis, where the lower torsional levels can be seen as vibrational states with quantum numbers v? exhibiting tunneling splitting, one finds that all operators generating matrix elements with ?v?=+/-1, or in general odd, work toward the formation of inverted splitting patterns, generating anomalous patterns.

Lattanzi, F.; di Lauro, C.

2004-01-01

26

Structural understanding of stabilization patterns in engineered bispecific Ig-like antibody molecules.  

PubMed

Bispecific immunoglobulin-like antibodies capable of engaging multiple antigens represent a promising new class of therapeutic agents. Engineering of these molecules requires optimization of the molecular properties of one of the domain components. Here, we present a detailed crystallographic and computational characterization of the stabilization patterns in the lymphotoxin-beta receptor (LTbetaR) binding Fv domain of an anti-LTbetaR/anti-TNF-related apoptosis inducing ligand receptor-2 (TRAIL-R2) bispecific immunoglobulin-like antibody. We further describe a new hierarchical structure-guided approach toward engineering of antibody-like molecules to enhance their thermal and chemical stability. PMID:19626705

Jordan, Jacob L; Arndt, Joseph W; Hanf, Karl; Li, Guohui; Hall, Janine; Demarest, Stephen; Huang, Flora; Wu, Xiufeng; Miller, Brian; Glaser, Scott; Fernandez, Erik J; Wang, Deping; Lugovskoy, Alexey

2009-12-01

27

Identifying molecular signatures in metal-molecule-metal junctions  

NASA Astrophysics Data System (ADS)

Single molecule identification in metal-molecule-metal junctions provides an ultimate probe that opens a new avenue for revolutionary advances in demonstrating single molecule device functions. Inelastic electron tunneling spectroscopy (IETS) is an ultra-sensitive method for probing vibrational characteristics of molecules with atomic resolution. State-of-the-art experiments on the inelastic transport in self-assembled monolayers of organic molecules have demonstrated the utility of the IETS technique to derive structural information concerning molecular conformations and contact configurations. Here we report the vibrational fingerprint of an individual ?-conjugated molecule sandwiched between gold nanoelectrodes. Our strategy combines analyses of single molecule conductance and vibrational spectra exploiting the nanofabricated mechanically-controllable break junction. We performed IETS measurements on 1,4-benzenedithiol and 2,5-dimercapto-1,3,4-thiadiazole to examine chemical discrimination at the single-molecule level. We found distinct IET spectra unique to the test molecules that agreed excellently with the Raman and theoretical spectra in the fingerprint region, and thereby succeeded in electrical identification of single molecule junctions.

Tsutsui, Makusu; Taniguchi, Masateru; Shoji, Kohei; Yokota, Kazumichi; Kawai, Tomoji

2009-09-01

28

Mechanically controlled molecular orbital alignment in single molecule junctions.  

PubMed

Research in molecular electronics often involves the demonstration of devices that are analogous to conventional semiconductor devices, such as transistors and diodes, but it is also possible to perform experiments that have no parallels in conventional electronics. For example, by applying a mechanical force to a molecule bridged between two electrodes, a device known as a molecular junction, it is possible to exploit the interplay between the electrical and mechanical properties of the molecule to control charge transport through the junction. 1,4'-Benzenedithiol is the most widely studied molecule in molecular electronics, and it was shown recently that the molecular orbitals can be gated by an applied electric field. Here, we report how the electromechanical properties of a 1,4'-benzenedithiol molecular junction change as the junction is stretched and compressed. Counterintuitively, the conductance increases by more than an order of magnitude during stretching, and then decreases again as the junction is compressed. Based on simultaneously recorded current-voltage and conductance-voltage characteristics, and inelastic electron tunnelling spectroscopy, we attribute this finding to a strain-induced shift of the highest occupied molecular orbital towards the Fermi level of the electrodes, leading to a resonant enhancement of the conductance. These results, which are in agreement with the predictions of theoretical models, also clarify the origins of the long-standing discrepancy between the calculated and measured conductance values of 1,4'-benzenedithiol, which often differ by orders of magnitude. PMID:22138861

Bruot, Christopher; Hihath, Joshua; Tao, Nongjian

2011-12-04

29

Empirical LCAO parameters for ? molecular orbitals in planar organic molecules  

Microsoft Academic Search

A novel parametrization within a simplified LCAO model (a type of Hückel model) is presented for the description of ? molecular orbitals in organic molecules containing ?-bonds between carbon, nitrogen, or oxygen atoms with sp hybridization. It is shown that the model is quite accurate in predicting the energy of the highest occupied ? orbital and the first ?–?* transition

L. G. D. Hawke; G. Kalosakas; C. Simserides

2009-01-01

30

Molecular orbital theory of ballistic electron transport through molecules  

NASA Astrophysics Data System (ADS)

Electron transport through molecules occurs, for instance, in STM imaging and in conductance measurements on molecular electronic devices (MEDs). To model these phenomena, we use a non-Hermitian model Hamiltonian [1] for the description of open systems that exchange current density with their environment. We derive qualitative, molecular-orbital-based rules relating molecular structure and conductance. We show how side groups attached to molecular conductors [2] can completely suppress the conductance. We discuss interference effects in aromatic molecules [3] that can also inhibit electron transport. Rules are developed [1] for the prediction of Fano resonances. All these phenomena are explained with a molecular orbital theory [1,4] for molecules attached to macroscopic reservoirs. [1] F. Goyer, M. Ernzerhof, and M. Zhuang, JCP 126, 144104 (2007); M. Ernzerhof, JCP 127, 204709 (2007). [2] M. Ernzerhof, M. Zhuang, and P. Rocheleau, JCP 123, 134704 (2005); G. C. Solomon, D Q. Andrews, R P. Van Duyne, and M A. Ratner, JACS 130, 7788 (2008). [3] M. Ernzerhof, H. Bahmann, F. Goyer, M. Zhuang, and P. Rocheleau, JCTC 2, 1291 (2006); G. C. Solomon, D. Q. Andrews, R. P. Van Duyne, and M. A. Ratner, JCP 129, 054701 (2008). [4] B.T. Pickup, P.W. Fowler, CPL 459, 198 (2008); P. Rocheleau and M. Ernzerhof, JCP, submitted.

Ernzerhof, Matthias; Rocheleau, Philippe; Goyer, Francois

2009-03-01

31

An extracellular adhesion molecule complex patterns dendritic branching and morphogenesis.  

PubMed

Robust dendrite morphogenesis is a critical step in the development of reproducible neural circuits. However, little is known about the extracellular cues that pattern complex dendrite morphologies. In the model nematode Caenorhabditis elegans, the sensory neuron PVD establishes stereotypical, highly branched dendrite morphology. Here, we report the identification of a tripartite ligand-receptor complex of membrane adhesion molecules that is both necessary and sufficient to instruct spatially restricted growth and branching of PVD dendrites. The ligand complex SAX-7/L1CAM and MNR-1 function at defined locations in the surrounding hypodermal tissue, whereas DMA-1 acts as the cognate receptor on PVD. Mutations in this complex lead to dramatic defects in the formation, stabilization, and organization of the dendritic arbor. Ectopic expression of SAX-7 and MNR-1 generates a predictable, unnaturally patterned dendritic tree in a DMA-1-dependent manner. Both in vivo and in vitro experiments indicate that all three molecules are needed for interaction. PMID:24120131

Dong, Xintong; Liu, Oliver W; Howell, Audrey S; Shen, Kang

2013-10-10

32

Direct mask-free patterning of molecular organic semiconductors using organic vapor jet printing  

Microsoft Academic Search

We demonstrate the solvent-free, high-resolution direct printing of molecular organic semiconductors for use in low cost optoelectronic applications. In this method, called organic vapor jet printing, hot inert carrier gas picks up the molecular organic vapor and expands it through a microscopic nozzle, resulting in physisorption of the molecules onto a cooled substrate. Pattern resolution and printing speed are determined

Max Shtein; Peter Peumans; Jay B. Benziger; Stephen R. Forrest

2004-01-01

33

Molecular surface analysis by laser ionization of desorbed molecules  

NASA Astrophysics Data System (ADS)

While elemental analysis of surfaces has progressed dramatically over the past ten years, quantitative molecular surface analysis remains difficult. This is particularly true in the analysis of complex materials such as polymers and rubbers which contain a wide compliment of additives and pigments to enhance their material characteristics. For mass spectrometric analysis the difficulty is two fold. First, desorption of surface molecules must be accompanied with minimal fragmentation and collateral surface damage. Second, the desorbed molecules must be ionized for subsequent mass analysis with high efficiency and without significant cracking. This paper focuses on the second of these problems.

Pellin, M. J.; Lykke, K. R.; Wurz, P.; Parker, D. H.

34

Imaging of Flow Patterns with Fluorescent Molecular Rotors  

PubMed Central

Molecular rotors are a group of fluorescent molecules that form twisted intramolecular charge transfer states (TICT) upon photoexcitation. Some classes of molecular rotors, among them those that are built on the benzylidene malononitrile motif, return to the ground state either by nonradiative intramolecular rotation or by fluorescence emission. In low-viscosity solvents, intramolecular rotation dominates, and the fluorescence quantum yield is low. Higher solvent viscosities reduce the intramolecular rotation rate, thus increasing the quantum yield. We recently described a different mechanism whereby the fluorescence quantum yield of the molecular rotor also depends on the shear stress of the solvent. In this study, we examined a possible application for shear-sensitive molecular rotors for imaging flow patterns in fluidic chambers. Flow chambers with different geometries were constructed from polycarbonate or acrylic. Solutions of molecular rotors in ethylene glycol were injected into the chamber under controlled flow rates. LED-induced fluorescence (LIF) images of the flow chambers were taken with a digital camera, and the intensity difference between flow and no-flow images was visualized and compared to computed fluid dynamics (CFD) simulations. Intensity differences were detectable with average flow rates as low as 0.1 mm/s, and an exponential association between flow rate and intensity increase was found. Furthermore, a good qualitative match to computed fluid dynamics simulations was seen. On the other hand, prolonged exposure to light reduced the emission intensity. With its high sensitivity and high spatial and temporal resolution, imaging of flow patterns with molecular rotors may become a useful tool in microfluidics, flow measurement, and control.

Mustafic, Adnan; Huang, Hsuan-Ming; Theodorakis, Emmanuel A.

2010-01-01

35

Molecular Design of Branched and Binary Molecules at Ordered Interfaces  

SciTech Connect

This study examined five different branched molecular architectures to discern the effect of design on the ability of molecules to form ordered structures at interfaces. Photochromic monodendrons formed kinked packing structures at the air-water interface due to the cross-sectional area mismatch created by varying number of alkyl tails and the hydrophilic polar head group. The lower generations formed orthorhombic unit cell with long range ordering despite the alkyl tails tilted to a large degree. Favorable interactions between liquid crystalline terminal groups and the underlying substrate were observed to compel a flexible carbosilane dendrimer core to form a compressed elliptical conformation which packed stagger within lamellae domains with limited short range ordering. A twelve arm binary star polymer was observed to form two dimensional micelles at the air-water interface attributed to the higher polystyrene block composition. Linear rod-coil molecules formed a multitude of packing structures at the air-water interface due to the varying composition. Tree-like rod-coil molecules demonstrated the ability to form one-dimensional structures at the air-water interface and at the air-solvent interface caused by the preferential ordering of the rigid rod cores. The role of molecular architecture and composition was examined and the influence chemically competing fragments was shown to exert on the packing structure. The amphiphilic balance of the different molecular series exhibited control on the ordering behavior at the air-water interface and within bulk structures. The shell nature and tail type was determined to dictate the preferential ordering structure and molecular reorganization at interfaces with the core nature effect secondary.

Kirsten Larson Genson

2005-12-27

36

Molecular design of branched and binary molecules at ordered interfaces  

NASA Astrophysics Data System (ADS)

This study examined five different branched molecular architectures to discern the effect of design on the ability of molecules to form ordered structures at interfaces. Photochromic monodendrons formed kinked packing structures at the air-water interface due to the cross sectional area mismatch created by varying number of alkyl tails and the hydrophilic polar head group. The lower generations formed orthorhombic unit cell with long range ordering despite the alkyl tails tilted to a large degree. Favorable interactions between liquid crystalline terminal groups and the underlying substrate were observed to compel a flexible carbosilane dendrimer core to form a compressed elliptical conformation which packed stagger within lamellae domains with limited short range ordering. A twelve arm binary star polymer was observed to form two dimensional micelles at the air-water interface attributed to the higher polystyrene block composition. Linear rod-coil molecules formed a multitude of packing structures at the air-water interface due to the varying composition. Tree-like rod-coil molecules demonstrated the ability to form one-dimensional structures at the air-water interface and at the air-solvent interface caused by the preferential ordering of the rigid rod cores. The role of molecular architecture and composition was examined and the influence chemically competing fragments was shown to exert on the packing structure. The amphiphilic balance of the different molecular series exhibited control on the ordering behavior at the air-water interface and within bulk structures. The shell nature and tail type was determined to dictate the preferential ordering structure and molecular reorganization at interfaces with the core nature effect secondary.

Genson, Kirsten Larson

37

Reactive Molecular Dynamics of Hypervelocity Collisions of PETN Molecules  

NASA Astrophysics Data System (ADS)

Born-Oppenheimer direct dynamics classical trajectory simulations of bimolecular collisions of PETN molecules have been performed to investigate the fundamental mechanisms of hypervelocity chemistry relevant to initiating reactions immediately behind the shock wavefront in energetic molecular crystals. The solid-state environment specifies the initial orientations of colliding molecules. The threshold velocities for initiating chemistry for a variety of crystallographic orientations were correlated with available experimental data on anisotropic shock sensitivity of PETN. Collisions normal to the planes (001) and (110) were found to be most sensitive with threshold velocities on the order of characteristic particle velocities in detonating PETN. The production of NO2 is the dominant reaction pathway in most of the reactive cases. The simulations show that the reactive chemistry, driven by dynamics rather than temperature during hypervelocity collisions, can occur at a very short time scale (10-13 s) under highly nonequilibrium conditions.

Landerville, A. C.; Oleynik, I. I.; White, C. T.

2009-10-01

38

Reactive molecular dynamics of hypervelocity collisions of PETN molecules.  

PubMed

Born-Oppenheimer direct dynamics classical trajectory simulations of bimolecular collisions of PETN molecules have been performed to investigate the fundamental mechanisms of hypervelocity chemistry relevant to initiating reactions immediately behind the shock wavefront in energetic molecular crystals. The solid-state environment specifies the initial orientations of colliding molecules. The threshold velocities for initiating chemistry for a variety of crystallographic orientations were correlated with available experimental data on anisotropic shock sensitivity of PETN. Collisions normal to the planes (001) and (110) were found to be most sensitive with threshold velocities on the order of characteristic particle velocities in detonating PETN. The production of NO2 is the dominant reaction pathway in most of the reactive cases. The simulations show that the reactive chemistry, driven by dynamics rather than temperature during hypervelocity collisions, can occur at a very short time scale (10(-13) s) under highly nonequilibrium conditions. PMID:19817467

Landerville, A C; Oleynik, I I; White, C T

2009-11-01

39

Molecular properties of selected diatomic molecules of astrophysical interest  

NASA Astrophysics Data System (ADS)

Molecular properties such as bond length, dipole moment, harmonic frequency, IR intensity, atomization energy, electron affinity and ionization potential of the selected diatomic molecules of astrophysical interest have been studied using hybrid density functional HF/DF B3LYP method. The consistency and convergence of the results have been tested with four basis sets from 6-311 + + G (2df, 2pd) to aug-cc-pVTZ with improved size and quality. Most of the results for dipole moment, harmonic frequency, IR intensity, electron affinity and ionization potential are new. The reported results agree well with theoretical and experimental data wherever available.

Midda, S.; Das, A. K.

2003-11-01

40

Microscopic approach to the kinetics of pattern formation of charged molecules on surfaces.  

PubMed

A microscopic formalism based on computing many-particle densities is applied to the analysis of the diffusion-controlled kinetics of pattern formation in oppositely charged molecules on surfaces or adsorbed at interfaces with competing long-range Coulomb and short-range Lennard-Jones interactions. Particular attention is paid to the proper molecular treatment of energetic interactions driving pattern formation in inhomogeneous systems. The reverse Monte Carlo method is used to visualize the spatial molecular distribution based on the calculated radial distribution functions (joint correlation functions). We show the formation of charge domains for certain combinations of temperature and dynamical interaction parameters. The charge segregation evolves into quasicrystalline clusters of charges, due to the competing long- and short-range interactions. The clusters initially co-exist with a gas phase of charges that eventually add to the clusters, generating "fingers" or line of charges of the same sign, very different than the nanopatterns expected by molecular dynamics in systems with competing interactions in two dimensions, such as strain or dipolar versus van der Waals interactions. PMID:20866821

Kuzovkov, V N; Zvejnieks, G; Kotomin, E A; Olvera de la Cruz, M

2010-08-09

41

Optical molecular imaging for systems biology: from molecule to organism  

PubMed Central

The development of highly efficient analytical methods capable of probing biological systems at system level is an important task that is required in order to meet the requirements of the emerging field of systems biology. Optical molecular imaging (OMI) is a very powerful tool for studying the temporal and spatial dynamics of specific biomolecules and their interactions in real time in vivo. In this article, recent advances in OMI are reviewed extensively, such as the development of molecular probes that make imaging brighter, more stable and more informative (e.g., FPs and semiconductor nanocrystals, also referred to as quantum dots), the development of imaging approaches that provide higher resolution and greater tissue penetration, and applications for measuring biological events from molecule to organism level, including gene expression, protein and subcellular compartment localization, protein activation and interaction, and low-mass molecule dynamics. These advances are of great significance in the field of biological science and could also be applied to disease diagnosis and pharmaceutical screening. Further developments in OMI for systems biology are also proposed.

Du, Wei; Wang, Ying; Luo, Qingming

2006-01-01

42

Fermion Molecular Dynamics for Rearrangement Collisions with Simple Molecules  

NASA Astrophysics Data System (ADS)

The Fermion Molecular Dynamics (FMD) method enables an all-electron treatment of reactive scattering using quasiclassical theory.(J.S. Cohen, Phys. Rev. A 54), 573 (1996); 56, 3583 (1997). It has previously been applied to ion-atom collisions and to atoms in strong laser fields. Here it is extended to molecular targets. A simple effective potential is found to provide a useful quasiclassical description of the hydrogen molecule. In particular, it is applied to capture of negative particles (barp and ?^-) by the hydrogen molecule. In contrast to the case with the same atomic targets, strong effects of the target isotope and projectile mass have been found. Negative particles having kinetic energies up to 100 eV are captured while the atomic capture cross sections cut off rapidly above 14 eV (in the c.m. system). The difference is due to the influence of ro-vibrational excitation, in addition to the electronic excitation also possible for atomic targets. Angular scattering distributions, needed for designing a proposed experiment, have been evaluated.

Cohen, J. S.

1998-05-01

43

Small-Molecule Hormones: Molecular Mechanisms of Action  

PubMed Central

Small-molecule hormones play crucial roles in the development and in the maintenance of an adult mammalian organism. On the molecular level, they regulate a plethora of biological pathways. Part of their actions depends on their transcription-regulating properties, exerted by highly specific nuclear receptors which are hormone-dependent transcription factors. Nuclear hormone receptors interact with coactivators, corepressors, basal transcription factors, and other transcription factors in order to modulate the activity of target genes in a manner that is dependent on tissue, age and developmental and pathophysiological states. The biological effect of this mechanism becomes apparent not earlier than 30–60 minutes after hormonal stimulus. In addition, small-molecule hormones modify the function of the cell by a number of nongenomic mechanisms, involving interaction with proteins localized in the plasma membrane, in the cytoplasm, as well as with proteins localized in other cellular membranes and in nonnuclear cellular compartments. The identity of such proteins is still under investigation; however, it seems that extranuclear fractions of nuclear hormone receptors commonly serve this function. A direct interaction of small-molecule hormones with membrane phospholipids and with mRNA is also postulated. In these mechanisms, the reaction to hormonal stimulus appears within seconds or minutes.

Budzinska, Monika

2013-01-01

44

Patterning small-molecule biocapture surfaces: microcontact insertion printing vs. photolithography.  

PubMed

Chemical patterns prepared by self-assembly, combined with soft lithography or photolithography, are directly compared. Pattern fidelity can be controlled in both cases but patterning at the low densities necessary for small-molecule probe capture of large biomolecule targets is better accomplished using microcontact insertion printing (?CIP). Surfaces patterned by ?CIP are used to capture biomolecule binding partners for the small molecules dopamine and biotin. PMID:21874174

Shuster, M J; Vaish, A; Cao, H H; Guttentag, A I; McManigle, J E; Gibb, A L; Martinez-Rivera, M; Martinez, M M; Nezarati, R M; Hinds, J M; Liao, W-S; Weiss, P S; Andrews, A M

2011-08-26

45

Commensurability and Mobility in Two-Dimensional Molecular Patterns on Graphite  

Microsoft Academic Search

Two-dimensional molecular patterns were obtained by the adsorption of long-chain alkanes, alcohols, fatty acids, and a dialkylbenzene from organic solutions onto the basal plane of graphite. In sim scanning tunneling microscopy (STM) studies revealed that these molecules organize in lamellae with the extended alkyl chains oriented parallel to a lattice axis within the basal plane of graphite. The planes of

Jurgen P. Rabe; Stefan Buchholz

1991-01-01

46

Gas-Phase Molecular Dynamics: Vibrational Dynamics of Polyatomic Molecules  

SciTech Connect

The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions and properties of short-lived chemical intermediates. High-resolution, high-sensitivity, laser absorption methods are augmented by high- temperature, flow-tube reaction kinetics studies with mass-spectrometic sampling. These experiments provide information on the energy levels, structures and reactivity of molecular free radical species and in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals involved in chemical systems. The experimental work is supported by theoretical studies using time-dependent quantum wavepacket calculations, which provide insight into energy flow among the vibrational modes of polyatomic molecules and interference effects in multiple-surface dynamics.

Muckerman, J.T.

1999-05-21

47

GAS-PHASE MOLECULAR DYNAMICS: VIBRATIONAL DYNAMICS OF POLYATOMIC MOLECULES  

SciTech Connect

The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions and properties of short-lived chemical intermediates. High-resolution, high-sensitivity, laser absorption methods are augmented by high-temperature, flow-tube reaction kinetics studies with mass-spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular free radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in radicals involved in chemical systems. The experimental work is supported by theoretical studies using time-dependent quantum wavepacket calculations, which provide insight into energy flow among the vibrational modes of polyatomic molecules and interference effects in multiple-surface dynamics.

MUCKERMAN,J.T.

1999-06-09

48

Molecular Analysis of Thymopentin Binding to HLA-DR Molecules  

PubMed Central

Thymopentin (TP5) triggers an immune response by contacting with T cells; however the molecular basis of how TP5 achieves this process remains incompletely understood. According to the main idea of immunomodulation, we suppose that it would be necessary for TP5 to form complex with human class II major histocompatibility complex DR molecules (HLA-DR) before TP5 interacts with T cells. The uptake of TP5 by EBV-transformed B cells expressing HLA-DR molecules and the histogram of fluorescence intensities were observed by using fluorescent- labeled TP5, testifying the direct binding of TP5 to HLA-DR. The binding specificity was confirmed by the inhibition with unlabeled TP5, suggesting the recognition of TP5 by HLA-DR. To confirm the interaction between TP5 and HLA-DR, the complex formation was predicted by using various modeling strategies including six groups of trials with different parameters, alanine substitutions of TP5, and the mutants of HLA-DR. The results demonstrated that TP5 and its alanine substitutions assumed distinct conformations when they bound to HLA-DR. The observation further showed that there was flexibility in how the peptide bound within the binding cleft. Also, the molecular analysis supplemented a newly important discovery to the effect of Val anchor on TP5 binding HLA-DR, and revealed the important effects of Glu11 and Asn62 on the recognition of TP5. These results demonstrated the capability of TP5 to associate with HLA-DR in living antigen presenting cells (APC), thereby providing a new and promising strategy to understand the immunomodulation mechanism induced by TP5 and to design potential immunoregulatory polypeptides.

Liu, Zuojia; Zheng, Xiliang; Wang, Jin; Wang, Erkang

2007-01-01

49

Patterns of energy levels and spectra for polyatomic molecules  

SciTech Connect

Laser spectroscopy has revealed a remarkable intricacy in the rotational, vibrational, and electronic energy levels for polyatomic molecules. The infrared spectra of SF/sub 6/, CF/sub 4/, and related molecules contain several levels of structure on top of structure which resembles a fractal in some ways. The purpose of this article will be to exhibit some of this structure and introduce the simplest theoretical interpretations of it which are presently available.

Harter, W.G.

1983-01-01

50

Simple molecular model for the binding of antibiotic molecules to bacterial ion channels  

NASA Astrophysics Data System (ADS)

A molecular model aimed at explaining recent experimental data by Nestorovich et al. [Proc. Natl. Acad. Sci. USA 99, 9789 (2002)] on the interaction of ampicillin molecules with the constriction zone in a channel of the general bacterial porin, OmpF (outer membrane protein F), is presented. The model extends T. L. Hill's theory for intermolecular interactions in a pair of binding sites [J. Am. Chem. Soc. 78, 3330 (1956)] by incorporating two binding ions and two pairs of interacting sites. The results provide new physical insights on the role of the complementary pattern of the charge distributions in the ampicillin molecule and the narrowest part of the channel pore. Charge matching of interacting sites facilitates drug binding. The dependence of the number of ampicillin binding events per second with the solution pH and salt concentration is explained qualitatively using a reduced number of fundamental concepts.

Mafé, Salvador; Ramírez, Patricio; Alcaraz, Antonio

2003-10-01

51

Single kinesin molecules studied with a molecular force clamp  

NASA Astrophysics Data System (ADS)

Kinesin is a two-headed, ATP-driven motor protein that moves processively along microtubules in discrete steps of 8nm, probably by advancing each of its heads alternately in sequence. Molecular details of how the chemical energy stored in ATP is coupled to mechanical displacement remain obscure. To shed light on this question, a force clamp was constructed, based on a feedback-driven optical trap capable of maintaining constant loads on single kinesin motors. The instrument provides unprecedented resolution of molecular motion and permits mechanochemical studies under controlled external loads. Analysis of records of kinesin motion under variable ATP concentrations and loads revealed several new features. First, kinesin stepping appears to be tightly coupled to ATP hydrolysis over a wide range of forces, with a single hydrolysis per 8-nm mechanical advance. Second, the kinesin stall force depends on the ATP concentration. Third, increased loads reduce the maximum velocity as expected, but also raise the apparent Michaelis-Menten constant. The kinesin cycle therefore contains at least one load-dependent transition affecting the rate at which ATP molecules bind and subsequently commit to hydrolysis. It is likely that at least one other load-dependent rate exists, affecting turnover number. Together, these findings will necessitate revisions to our understanding of how kinesin motors function.

Visscher, Koen; Schnitzer, Mark J.; Block, Steven M.

1999-07-01

52

ION AND MOLECULE SENSORS USING MOLECULAR RECOGNITION IN LUMINESCENT, CONDUCTIVE POLYMERS  

EPA Science Inventory

This program integrates three individual, highly interactive projects that will use molecular recognition strategies to develop sensor technology based on luminescent, conductive polymers that contain sites for binding specific molecules or ions in the presence of related molecul...

53

MAMP (microbe-associated molecular pattern) triggered immunity in plants  

PubMed Central

Plants are sessile organisms that are under constant attack from microbes. They rely on both preformed defenses, and their innate immune system to ward of the microbial pathogens. Preformed defences include for example the cell wall and cuticle, which act as physical barriers to microbial colonization. The plant immune system is composed of surveillance systems that perceive several general microbe elicitors, which allow plants to switch from growth and development into a defense mode, rejecting most potentially harmful microbes. The elicitors are essential structures for pathogen survival and are conserved among pathogens. The conserved microbe-specific molecules, referred to as microbe- or pathogen-associated molecular patterns (MAMPs or PAMPs), are recognized by the plant innate immune systems pattern recognition receptors (PRRs). General elicitors like flagellin (Flg), elongation factor Tu (EF-Tu), peptidoglycan (PGN), lipopolysaccharides (LPS), Ax21 (Activator of XA21-mediated immunity in rice), fungal chitin, and ?-glucans from oomycetes are recognized by plant surface localized PRRs. Several of the MAMPs and their corresponding PRRs have, in recent years, been identified. This review focuses on the current knowledge regarding important MAMPs from bacteria, fungi, and oomycetes, their structure, the plant PRRs that recognizes them, and how they induce MAMP-triggered immunity (MTI) in plants.

Newman, Mari-Anne; Sundelin, Thomas; Nielsen, Jon T.; Erbs, Gitte

2013-01-01

54

Molecular dynamics simulations of lubricant spreading on lubricant-patterned substrates  

NASA Astrophysics Data System (ADS)

The spreading of nonfunctional perfluoropolyether (PFPE) on PFPE-patterned substrates is examined using molecular dynamics simulations. During the spreading process, mobile molecules will encounter, pass by, and embrace the bonded ones. The movement of mobile molecules is hindered by the bonded ones. The spreading exhibits a slow evolution with time, a steep profile with a precursor film from a side view and a complicated profile from a top-down view. The atomic-scale mechanism is analyzed by the driving term, such as the van der Waals interaction and surface diffusion, and the resistance term, such as the interaction between bonded and mobile molecules or, furthermore, the combined interaction from the adjacent bonded molecules. Besides, the spreading profiles of PFPE on PFPE-patterned substrates with different coverage ratios are compared, which indicate that the coverage ratio has significant effects on the PFPE spreading behavior.

Li, Xin; Hu, Yuanzhong; Ma, Tianbao; Wang, Hui; Zhang, Jun

2006-10-01

55

Single-Electron Molecular Transistors on the Base of Various Types of Cluster Molecules.  

National Technical Information Service (NTIS)

Effect of single-electron tunneling in double-junction tunnel system based on single molecule was investigated. Molecular single-electron transistor was demonstrated. The comparison of measured characteristics with the similar characteristics of molecular...

E. S. Soldatov A. S. Trifonov S. P. Gubin V. V. Khanin G. B. Khomutov

1999-01-01

56

Structural and dynamic roles of permanent water molecules in ligand molecular recognition by chicken liver bile acid binding protein.  

PubMed

Chicken liver bile acid binding protein (cL-BABP) crystallizes with water molecules in its binding site. To obtain insights on the role of internal water, we performed two 100 ns molecular dynamics (MD) simulations in explicit solvent for cL-BABP, as apo form and as a complex with two molecules of cholic acid, and analyzed in detail the dynamics properties of all water molecules. The diffusion coefficients of the more persistent internal water molecules are significantly different from the bulk, but similar between the two protein forms. A different number of molecules and a different organization are observed for apo- and holo-cL-BABP. Most water molecules identified in the binding site of the apo-crystal diffuse to the bulk during the simulation. In contrast, almost all the internal waters of the holo-crystal maintain the same interactions with internal sidechains and ligands, which suggests they have a relevant role in protein-ligand molecular recognition. Only in the presence of these water molecules we were able to reproduce, by a classical molecular docking approach, the structure of the complex cL-BABP::cholic acid with a low ligand root mean square deviation (RMSD) with respect to its reference positioning. Literature data reported a conserved pattern of hydrogen bonds between a single water molecule and three amino acid residues of the binding site in a series of crystallized FABP. In cL-BABP, the interactions between this conserved water molecule and the three residues are present in the crystal of both apo- and holo-cL-BABP but are lost immediately after the start of molecular dynamics. PMID:18654997

Ricchiuto, Piero; Rocco, Alessandro Guerini; Gianazza, Elisabetta; Corrada, Dario; Beringhelli, Tiziana; Eberini, Ivano

57

RNA templating of molecular assembly and covalent modification patterning in early molecular evolution and modern biosystems.  

PubMed

The Direct RNA Template (DRT) hypothesis proposes that an early stage of genetic code evolution involved RNA molecules acting as stereochemical recognition templates for assembly of specific amino acids in sequence-ordered arrays, providing a framework for directed covalent peptide bond formation. It is hypothesized here that modern biological precedents may exist for RNA-based structural templating with functional analogies to hypothetical DRT systems. Beyond covalent molecular assembly, an extension of the DRT concept can include RNA molecules acting as dynamic structural template guides for the specific non-covalent assembly of multi-subunit complexes, equivalent to structural assembly chaperones. However, despite numerous precedents for RNA molecules acting as scaffolds for protein complexes, true RNA-mediated assembly chaperoning appears to be absent in modern biosystems. Another level of function with parallels to a DRT system is possible if RNA structural motifs dynamically guided specific patterns of catalytic modifications within multiple target sites in a pre-formed polymer or macromolecular complex. It is suggested that this type of structural RNA templating could logically play a functional role in certain areas of biology, one of which is the glycome of complex organisms. If any such RNA templating processes are shown to exist, they would share no necessary evolutionary relationships with events during early molecular evolution, but may promote understanding of the practical limits of biological RNA functions now and in the ancient RNA World. Awareness of these formal possibilities may also assist in the current search for functions of extensive non-coding RNAs in complex organisms, or for efforts towards artificial rendering of DRT systems. PMID:21703277

Dunn, Ian S

2011-06-17

58

Signatures of molecular magnetism in single-molecule transport spectroscopy.  

PubMed

We report single-molecule-transistor measurements on devices incorporating magnetic molecules. By studying the electron-tunneling spectrum as a function of magnetic field, we are able to identify signatures of magnetic states and their associated magnetic anisotropy. A comparison of the data to simulations also suggests that sequential electron tunneling may enhance the magnetic relaxation of the magnetic molecule. PMID:16968018

Jo, Moon-Ho; Grose, Jacob E; Baheti, Kanhayalal; Deshmukh, Mandar M; Sokol, Jennifer J; Rumberger, Evan M; Hendrickson, David N; Long, Jeffrey R; Park, Hongkun; Ralph, D C

2006-09-01

59

Changing Patterns of Cell Adhesion Molecules during Mouse Pelage Hair Follicle Development  

Microsoft Academic Search

The morphogenesis of hairs is initiated and maintained by reciprocal interactions between groups of epithelial and mesenchymal cells. To examine whether cell adhesion molecules play a role in this process, prenatal distribution patterns of various cell adhesion molecules were studied during hair follicle morphogenesis in the dorsal skin of C57BL mouse embryos, using monoclonal antibodies. E-cadherin was present on all

M. H. Hardy; U. Vielkind

1996-01-01

60

Diffusible signal molecules controlling cell differentiation and patterning in Dictyostelium.  

PubMed

Slime moulds, such as Dictyostelium discoideum, have biochemical, physiological and probably developmental features in common with both plants and animals. During development separate Dictyostelium amoebae first aggregate into collecting centers to form small multicellular organisms which, in their slug form, can migrate over the substratum toward light. Eventually a slug culminates to form a fruiting body consisting of a cellular stalk supporting a mass of spores. Development is highly regulative, indicating that it is controlled by signalling between the cells. A number of diffusible signal molecules have been discovered, including cyclic AMP, the chemoattractant in aggregation, and DIF-1, a novel chlorinated phenyl alkanone, which acts as a specific inducer of stalk cell differentiation. The migrating slug contains three types of precursor cell: prespore, prestalk A and prestalk B cells. Differentiation of these cells from uncommitted amoebae can be brought about in cell cultures by cyclic AMP and DIF-1 acting in combination: cyclic AMP alone favours prespore, DIF-1 alone favours prestalk B, cyclic AMP and DIF-1 together favour prestalk A cell differentiation. There is evidence suggesting that these signals act in the same way in the intact aggregate. A cytoplasmic DIF-1 binding protein has been discovered, whose level increases as cells become sensitive to DIF-1 and which binds DIF-1 with an affinity and specificity suggestive of a receptor. At the same time, cells are able to inactivate DIF-1 by a metabolic pathway involving at least 12 metabolites. Metabolism may also serve to produce gradients of DIF-1 in the aggregate or other signal molecules from DIF-1.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:1660326

Berks, M; Traynor, D; Carrin, I; Insall, R H; Kay, R R

1991-01-01

61

XXI. The formation of molecular aggregates in radon-gas mixtures containing polar molecules  

Microsoft Academic Search

By various methods gaseous mixtures containing radon and its decay products have been investigated for the presence of molecular aggregates. Since in every case studied aggregates were obtained when the mixture contained polar molecules, and since in no case were aggregates detected when only non-polar molecules were present, it would appear that polar molecules definitely favour and are possibly essential

E. L. Harrington; O. A. Gratias

1931-01-01

62

Speckle Patterns with Atomic and Molecular de Broglie Waves  

SciTech Connect

We have developed a nozzle source that delivers a continuous beam of atomic helium or molecular hydrogen having a high degree of transverse coherence and with adequate optical brightness to enable new kinds of experiments. Using this source we have measured single slit diffraction patterns and the first ever speckle-diffraction patterns using atomic and molecular de Broglie waves. Our results suggest fruitful application of coherent matter beams in dynamic scattering and diffractive imaging at short wavelength and with extreme surface sensitivity.

Patton, Forest S.; Deponte, Daniel P.; Kevan, Stephen D. [Department of Physics, University of Oregon, Eugene, Oregon 97403-1274 (United States); Elliott, Greg S. [Department of Physics, University of Puget Sound, Tacoma, Washington 98416 (United States)

2006-07-07

63

Complete Photo-Induced Breakup of the H2 Molecule as a Probe ofMolecular Electron Correlation  

SciTech Connect

Despite decades of progress in quantum mechanics, electron correlation effects are still only partially understood. Experiments in which both electrons are ejected from an oriented hydrogen molecule by absorption of a single photon have recently demonstrated a puzzling phenomenon: The ejection pattern of the electrons depends sensitively on the bond distance between the two nuclei as they vibrate in their ground state. Here we report a complete numerical solution of the Schrodinger equation for the double photoionization of H2. The results suggest that the distribution of photoelectrons emitted from aligned molecules reflects electron correlation effects that are purely molecular in origin.

Vanroose, Wim; Martin, Fernando; Rescigno, Thomas N.; McCurdy, C.William

2005-11-17

64

Vibrational symmetry classification and torsional tunneling splitting patterns in G6(EM), G12, and G36(EM) molecules  

NASA Astrophysics Data System (ADS)

It is shown that the torsional splitting patterns in methanol-like molecules, with the excitation of small amplitude vibrational modes in the methyl group, are determined by mechanisms that can be formulated in an almost identical fashion to that for ethane-like molecules. This is achieved by treating ethane-like molecules by the internal axis method (IAM) and methanol-like molecules by the principal axis method (PAM) or rho-axis method (RAM). Using the extended molecular groups G6(EM) or C6v(M) for methanol and G36(EM) for ethane, vibrations perpendicular to the internal rotation axis are conveniently described by modes of higher degeneracy (E for methanol and Gs for ethane) in the absence of coupling of top and frame. Head-tail coupling operators, except the cos-type barrier terms, lower the degeneracy, causing vibrational splittings. Coupled vibrational pairs with torsional splitting patterns that we call 'regular' (pure A1, A2 pairs for methanol and pure E1d, E2d pairs for ethane) or 'inverted' (pure B1, B2 pairs for methanol and pure E1s, E2s pairs for ethane) can be formed as limit cases. Actual splitting patterns occur between the above limits, and are basically determined by torsional Coriolis coupling, which can tune more or less to resonance pairs of uncoupled basis levels linked by specific head-tail coupling operators. The inversion of torsional splitting patterns, observed in perpendicular vibrational modes of the methyl group of methanol, can be predicted by these theoretical considerations. Similar considerations apply to molecules of G12 symmetry.

Lattanzi, F.; di Lauro, C.

65

Information theory, atoms in molecules, and molecular similarity  

PubMed Central

Using information theory, it is argued that from among possible definitions of what an atom is when it is in a molecule, a particular one merits special attention. Namely, it is the atom defined by the “stockholders partitioning” of a molecule invented by Hirshfeld [(1977) Theor. Chim. Acta 44, 129]. The theoretical tool used is the minimum entropy deficiency principle (minimum missing information principle) of Kullback and Liebler [(1951) Ann. Math. Stat. 22, 79]. A corresponding analysis is given of the problem of assessing similarity between molecules or pieces of molecules.

Nalewajski, Roman F.; Parr, Robert G.

2000-01-01

66

Molecular vibrations of methane molecules in the structure I clathrate hydrate from ab initio molecular dynamics simulation  

NASA Astrophysics Data System (ADS)

Vibrational frequencies of guest molecules in clathrate hydrates reflect the molecular environment and dynamical behavior of molecules. A detailed understanding of the mechanism for the vibrational frequency changes of the guest molecules in the clathrate hydrate cages is still incomplete. In this study, molecular vibrations of methane molecules in a structure I clathrate hydrate are calculated from ab initio molecular dynamics simulation. The vibrational spectra of methane are computed by Fourier transform of autocorrelation functions, which reveal distinct separation of each vibrational mode. Calculated symmetric and asymmetric stretching vibrational frequencies of methane molecules are lower in the large cages than in the small cages (8 and 16 cm-1 for symmetric and asymmetric stretching, respectively). These changes are closely linked with the C-H bond length. The vibrational frequencies for the bending and rocking vibrational modes nearly overlap in each of the cages.

Hiratsuka, Masaki; Ohmura, Ryo; Sum, Amadeu K.; Yasuoka, Kenji

2012-01-01

67

Molecular vibrations of methane molecules in the structure I clathrate hydrate from ab initio molecular dynamics simulation.  

PubMed

Vibrational frequencies of guest molecules in clathrate hydrates reflect the molecular environment and dynamical behavior of molecules. A detailed understanding of the mechanism for the vibrational frequency changes of the guest molecules in the clathrate hydrate cages is still incomplete. In this study, molecular vibrations of methane molecules in a structure I clathrate hydrate are calculated from ab initio molecular dynamics simulation. The vibrational spectra of methane are computed by Fourier transform of autocorrelation functions, which reveal distinct separation of each vibrational mode. Calculated symmetric and asymmetric stretching vibrational frequencies of methane molecules are lower in the large cages than in the small cages (8 and 16 cm(-1) for symmetric and asymmetric stretching, respectively). These changes are closely linked with the C-H bond length. The vibrational frequencies for the bending and rocking vibrational modes nearly overlap in each of the cages. PMID:22299892

Hiratsuka, Masaki; Ohmura, Ryo; Sum, Amadeu K; Yasuoka, Kenji

2012-01-28

68

Time-Resolved Molecular Frame Dynamics of Fixed-in-Space CS2 Molecules  

SciTech Connect

Random orientation of molecules within a sample leads to blurred observationsof chemical reactions studied from the laboratory perspective. Methodsdeveloped for the dynamic imaging of molecular structures and processesstruggle with this, as measurements are optimally made in the molecular frame.Here we uselaser alignment to transiently fix CS2 molecules in space longenough to elucidate, in the molecular reference frame, details of ultrafast electronic vibrationaldynamics during a photochemical reaction. These three-dimensional photoelectron imaging results, combined with ongoing efforts in molecular alignment and orientation, presage a wide range of insights obtainable fromtime-resolved studies in the molecular frame.

Bisgaard, Christer; Clarkin, Owen; Wu, Guorong; Lee, Anthony; Gessner, Oliver; Hayden, Carl; Stolow, Albert

2009-04-02

69

Molecular patterns in melanoma and therapeutic targets.  

PubMed

Malignant melanoma is one of the most lethal cancers whose treatment options are limited once it has metastasized. Recent advances in molecular technology have improved our understanding of the underlying mechanisms of melanoma pathogenesis. In this article, we highlight several pathways that have been implicated in melanoma-genesis. While a cure is not yet within grasp, the picture on the horizon is less hazy and the next decade promises to yield exciting new therapeutic discoveries. PMID:20930694

Chua, R A; Arbiser, J L

2010-10-01

70

Single Molecule Switches and Molecular Self-Assembly: Low Temperature STM Investigations and Manipulations  

SciTech Connect

This dissertation is devoted to single molecule investigations and manipulations of two porphyrin-based molecules, chlorophyll-a and Co-popphyrin. The molecules are absorbed on metallic substrates and studied at low temperatures using a scanning tunneling microscope. The electronic, structural and mechanical properties of the molecules are investigated in detail with atomic level precision. Chlorophyll-a is the key ingredient in photosynthesis processes while Co-porphyrin is a magnetic molecule that represents the recent emerging field of molecular spintronics. Using the scanning tunneling microscope tip and the substrate as electrodes, and the molecules as active ingredients, single molecule switches made of these two molecules are demonstrated. The first switch, a multiple and reversible mechanical switch, is realized by using chlorophyll-a where the energy transfer of a single tunneling electron is used to rotate a C-C bond of the molecule's tail on a Au(111) surface. Here, the det

Iancu, Violeta

2006-08-01

71

Identification of nonplanar small molecule for G-quadruplex grooves: molecular docking and molecular dynamic study.  

PubMed

DNA G-quadruplex is an attractive drug target for anticancer therapy. Most G-quadruplex ligands have little selectivity, due to ?-stacking interaction with common G-tetrads surface. Thanks to the varieties of G-quadruplex grooves, the groove-binding ligand is expected to create high selectivity. Therefore, developing novel molecular geometries that target G-quadruplex groove has been paid growing attention. In this work, steroid FG, a special nonplanar and nonaromatic small molecule, interacting with different conformations of G-quadruplexes has been studied by molecular docking and molecular dynamics simulations. The results showed the selectivity of the hydrophobic group of steroid FG for the wide groove of antiparallel G-quadruplex. The methyl groups on the tetracyclic ring of steroid represent the specific binding ability for the small hydrophobic cavity formed by reversed stacking of G-tetrads in antiparallel G-quadruplex groove. This work provides new insight for developing new classes of G-quadruplex groove-binding ligands. PMID:22018460

Li, Jinlian; Jin, Xiaoqiang; Hu, LiHong; Wang, Jianping; Su, Zhongmin

2011-10-05

72

Molecular Forces for the Binding and Condensation of DNA Molecules  

Microsoft Academic Search

Atomic force microscopy has been used to investigate the binding between a double-stranded DNA and bilayers of cationic lipids and zwitterionic lipids in low ionic-strength solutions. The binding of a DNA molecule to freshly cleaved mica surface in solution has also been measured. The binding of DNA molecules to cationic lipid bilayers has a minimal strength of ?45pN. On zwitterionic

Xian-E. Cai; Jie Yang

2002-01-01

73

Molecular Physiology of Protein Kinases (and Phosphatases): Molecules, mechanisms, medicines  

NSDL National Science Digital Library

This recorded presentation from the 2011 EB Refresher Course on CellPhysiology:Intracellular Signaling addressed protein kinase structure, conformational changes, molecular domains, activation, and inhibition.

Michael Eck (Harvard University)

2011-04-09

74

Molecular Physiology of Protein Kinases (and Phosphatases): Molecules, mechanisms, medicines  

NSDL National Science Digital Library

This powerpoint presentation from the 2011 EB Refresher Course on CellPhysiology:Intracellular Signaling addressed protein kinase structure, conformational changes, molecular domains, activation, and inhibition.

Michael Eck (Harvard University)

2011-04-09

75

Correlated Rotational Alignment Spectroscopy of Isolated Molecules and Molecular Mixtures  

NASA Astrophysics Data System (ADS)

We present a novel multi-pulse spectroscopic method for the correlated analysis of molecular mass, rotational structure and electronic structure. First experiments investigate carbon disulfide and butadiene.

Schröter, C.; Kosma, K.; Schultz, T.

2013-03-01

76

Non-equilibrium molecular dynamics simulations of structured molecules  

NASA Astrophysics Data System (ADS)

Corresponding-states theories fail to predict the large difference observed between n-butane and isobutane viscosities at similar reduced conditions. To investigate the molecular cause of these structural effects upon viscosity, nonequilibrium molecular dynamics simulations of Lennard-Jones site-site models representing n-butane and isobutane are performed over much of the density range for which experimental data are available. Simulated viscosities at zero shear agree very well with experimental data over the entire density range. Site size, non-equilibrium molecular alignment and molecular geometry are the primary factors causing both the similarities and differences between the isomers' viscosity and rheology.

Rowley, Richard L.; Ely, James F.

77

Nanomechanical recognition measurements of individual DNA molecules reveal epigenetic methylation patterns.  

PubMed

Atomic force microscopy (AFM) is a powerful tool for analysing the shapes of individual molecules and the forces acting on them. AFM-based force spectroscopy provides insights into the structural and energetic dynamics of biomolecules by probing the interactions within individual molecules, or between a surface-bound molecule and a cantilever that carries a complementary binding partner. Here, we show that an AFM cantilever with an antibody tether can measure the distances between 5-methylcytidine bases in individual DNA strands with a resolution of 4 Å, thereby revealing the DNA methylation pattern, which has an important role in the epigenetic control of gene expression. The antibody is able to bind two 5-methylcytidine bases of a surface-immobilized DNA strand, and retracting the cantilever results in a unique rupture signature reflecting the spacing between two tagged bases. This nanomechanical approach might also allow related chemical patterns to be retrieved from biopolymers at the single-molecule level. PMID:21037576

Zhu, Rong; Howorka, Stefan; Pröll, Johannes; Kienberger, Ferry; Preiner, Johannes; Hesse, Jan; Ebner, Andreas; Pastushenko, Vassili Ph; Gruber, Hermann J; Hinterdorfer, Peter

2010-10-31

78

Three-dimensional Molecular Modeling with Single Molecule FRET  

PubMed Central

Single molecule fluorescence energy transfer experiments enable investigations of macromolecular conformation and folding by the introduction of fluorescent dyes at specific sites in the macromolecule. Multiple such experiments can be performed with different labeling site combinations in order to map complex conformational changes or interactions between multiple molecules. Distances that are derived from such experiments can be used for determination of the fluorophore positions by triangulation. When combined with a known structure of the macromolecule(s) to which the fluorophores are attached, a three-dimensional model of the system can be determined. However, care has to be taken to properly derive distance from fluorescence energy transfer efficiency and to recognize the systematic or random errors for this relationship. Here we review the experimental and computational methods used for three-dimensional modeling based on single molecule fluorescence resonance transfer, and describe recent progress in pushing the limits of this approach to macromolecular complexes.

Brunger, Axel T.; Strop, Pavel; Vrljic, Marija; Chu, Steven; Weninger, Keith R.

2011-01-01

79

A molecular platinum cluster junction: a single-molecule switch.  

PubMed

We present a theoretical study of electron transport through single-molecule junctions incorporating a Pt(6) metal cluster bound within an organic framework. The insertion of this molecule between a pair of electrodes leads to a fully atomically engineered nanometallic device with high conductance at the Fermi level and two sequential high on/off switching states. The origin of this property can be traced back to the existence of a degenerate HOMO consisting of two asymmetric orbitals with energies close to the Fermi level of the metal leads. The degeneracy is broken when the molecule is contacted to the leads, giving rise to two resonances that become pinned to the Fermi level and display destructive interference. PMID:23330549

Zotti, Linda A; Leary, Edmund; Soriano, Maria; Cuevas, Juan Carlos; Palacios, Juan Jose

2013-01-29

80

Electrostatic spin crossover in a molecular junction of a single-molecule magnet Fe{2}.  

PubMed

Spin crossover by means of an electric bias is investigated by spin-polarized density-functional theory calculations combined with the Keldysh nonequilibrium Green's technique in a molecular junction, where an individual single-molecule magnet Fe{2}(acpybutO)(O{2}CMe)(NCS){2} is sandwiched between two infinite Au(100) nanoelectrodes. Our study demonstrates that the spin crossover, based on the Stark effect, is achieved in this molecular junction under an electric bias but not in the isolated molecule under external electric fields. The main reason is that the polarizability of the molecular junction has an opposite sign to that of the isolated molecule, and thus from the Stark effect the condition for the spin crossover in the molecular junction is contrary to that in the isolated molecule. PMID:22304282

Hao, Hua; Zheng, XiaoHong; Song, LingLing; Wang, RuiNing; Zeng, Zhi

2012-01-05

81

Influence of molecular structure on plasma carbonization of organic semiconductor molecules  

NASA Astrophysics Data System (ADS)

The plasma treatment of organic semiconductor molecules includes issues related with nanoscale plasma interfaces. The process was examined by optical emission spectroscopy. It was found that molecules are sublimed by the heat and decomposed by the interaction with the plasma. The product carbon solids were examined by Raman spectroscopy. The raman spectra are strongly dependent on the molecular structures. The carbon solids which does not show graphitic Raman spectra have nanostructures originating from initial molecules.

Shimada, Toshihiro; Muraya, Naoki; Tomita, Jun; Yanase, Takashi; Nagahama, Taro

2013-06-01

82

Moving into the cell: single-molecule studies of molecular motors in complex environments  

Microsoft Academic Search

Much has been learned in the past decades about molecular force generation. Single-molecule techniques, such as atomic force microscopy, single-molecule fluorescence microscopy and optical tweezers, have been key in resolving the mechanisms behind the power strokes, 'processive' steps and forces of cytoskeletal motors. However, it remains unclear how single force generators are integrated into composite mechanical machines in cells to

Claudia Veigel; Christoph F. Schmidt

2011-01-01

83

Energy Levels, Selection Rules, and Line Intensities for Molecular Beam Electric Resonance Experiments with Diatomic Molecules  

Microsoft Academic Search

In the molecular beam electric resonance method the energy levels in an electric field of a diatomic molecule which is in the ground electronic state, and a low vibrational and rotational state are studied. Transitions are produced between states with different space quantization of the molecule relative to the electric field and with different couplings of the angular momenta of

Vernon Hughes; Ludwig Grabner

1950-01-01

84

Microcontact printing of axon guidance molecules for generation of graded patterns.  

PubMed

Microcontact printing (microCP) of proteins has been successfully used for patterning surfaces in various contexts. Here we describe a simple 'lift-off' method to print precise patterns of axon guidance molecules, which are used as substrate for growing chick retinal ganglion cell (RGC) axons. Briefly, the etched pattern of a silicon master is transferred to a protein-coated silicone cuboid (made from polydimethylsiloxane, PDMS), which is then used as a stamp on a glass coverslip. RGC explants are placed adjacent to the pattern and cultured overnight. Fluorescent labeling of the printed proteins allows the quantitative analysis of the interaction of axons and growth cones with single protein dots and of the overall outgrowth and guidance rate in variously designed patterns. Patterned substrates can be produced in 3-4 h and are stable for up to one week at 4 degrees C; the entire protocol can be completed in 3 d. PMID:17406418

von Philipsborn, Anne C; Lang, Susanne; Bernard, André; Loeschinger, Jürgen; David, Christian; Lehnert, Dirk; Bastmeyer, Martin; Bonhoeffer, Friedrich

2006-01-01

85

The Molecule Calculator: A Web Application for Fast Quantum Mechanics-Based Estimation of Molecular Properties  

NASA Astrophysics Data System (ADS)

A new web-server called The Molecule Calculator (MolCalc) is presented. The entry page is a molecular editor (JSmol) for interactive molecule building. The resulting structure can then be used to estimate molecular properties such as heats of formation and other thermodynamic properties, vibrational frequencies and vibrational modes, and molecular orbitals and orbital energies. These properties are computed using the GAMESS program at either the RHF/STO-3G (orbitals and orbital energies) or PM3 level of theory (all other properties) in a matter of seconds or minutes depending on the size of the molecule. The results, though approximate, can help students develop a "chemical intuition" about how molecular structure affects molecular properties, without performing the underlying calculations by hand, a near impossible task for all but the simplest chemical systems.

Jensen, Jan H.; Kromann, Jimmy C.

2013-08-01

86

Molecular polarizability in quantum defect theory: polar molecules  

SciTech Connect

The reduced-added Green's function technique in the quantum defect theory combines the advantages of analytical and ab initio methods in calculating frequency-dependent (dynamic) polarizabilities of atoms and molecules, providing an exact account for the high-excited and continuum electronic states. In the present paper this technique is modified to take into account the long-range dipole potential of a polar molecule core. The method developed is applied to calculation of the dynamic polarizability tensors of alkali-metal hydrides LiH and NaH as well as to some fluorides (CaF and BF) in the frequency range up to the first resonances. The results are in good agreement with ab initio calculations available for some frequencies.

Akindinova, E. V.; Chernov, V. E.; Kretinin, I. Yu.; Zon, B. A. [Voronezh State University, Voronezh RU-394693 (Russian Federation)

2010-04-15

87

Thermodynamics of Hydrogen Bond Patterns in Supramolecular Assemblies of Water Molecules  

Microsoft Academic Search

The PACHA (Partial Atomic Charges and Hardnesses Analysis) formalism is applied to various supramolecular assemblies of water molecules. After a detailed study of all available crystal structures for ice polymorphs, we shown that the hydrogen bond strength is roughly constant below 1 GPa and considerably weakened above that value. New hydrogen bond patterns are proposed for ice IV, V, and

Marc Henry

2002-01-01

88

Characterization of a pattern recognition molecule vitellogenin from carp ( Cyprinus carpio)  

Microsoft Academic Search

Pattern recognition proteins function in innate immune responses by binding to molecules on the surface of invading pathogens and initiating host defense reactions. To explore the role of vitellogenin (Vg) in fish innate immunity, we purified Vg from Carp by gel filtration combined with diethylaminoethyl (DEAE) chromatography. The purified Vg was confirmed by MALDI-TOF mass spectrometry. Antibacterial activity analysis showed

Qing-Hui Liu; Shi-Cui Zhang; Zhao-Jie Li; Chun-Ren Gao

2009-01-01

89

Molecular Evolution of Hemojuvelin and the Repulsive Guidance Molecule Family  

Microsoft Academic Search

Repulsive guidance molecules (RGMs) are found in vertebrates and chordates and are involved in embryonic development and iron\\u000a homeostasis. Members of this family are GPI-linked membrane proteins that contain an N-terminal signal peptide, a C-terminal\\u000a propeptide, and a conserved RGD motif. Vertebrates are known to possess three paralogues; RGMA and RGMB (sometimes called\\u000a Dragon) are expressed in the nervous system

Laura Marie Camus; Lisa A. Lambert

2007-01-01

90

Molecular forces for the binding and condensation of DNA molecules.  

PubMed

Atomic force microscopy has been used to investigate the binding between a double-stranded DNA and bilayers of cationic lipids and zwitterionic lipids in low ionic-strength solutions. The binding of a DNA molecule to freshly cleaved mica surface in solution has also been measured. The binding of DNA molecules to cationic lipid bilayers has a minimal strength of approximately 45 pN. On zwitterionic lipid bilayers and mica surface, the minimal binding strength is approximately twice that value. The binding also has a dynamic nature, with only a certain percentage of recorded force curves containing the binding characteristics. Divalent Mg(2+) ions enhance the binding by increasing that percentage without any effect on the binding strength. We have also observed a long-range attraction between DNA molecules and cationic lipid bilayers with a strength much larger than the minimum force and a range well over 50 nm, possibly related to the driving force responsible for the two-dimensional condensation of DNA. PMID:11751322

Cai, Xian-E; Yang, Jie

2002-01-01

91

Molecular flux dependence of chemical patterning by microcontact printing.  

PubMed

We address the importance of the dynamic molecular ink concentration at a polymer stamp/substrate interface during microcontact displacement or insertion printing. We demonstrate that by controlling molecular flux, we can influence both the molecular-scale order and the rate of molecular exchange of self-assembled monolayers (SAMs) on gold surfaces. Surface depletion of molecular ink at a polymer stamp/substrate interface is driven predominantly by diffusion into the stamp interior; depletion occurs briefly at the substrate by SAM formation, but diffusion of molecules into the bulk of the stamp dominates over practical experimental time scales. As contact time is increased, the interface concentration varies significantly due to diffusion, affecting the quality and coverage of printed films. Controlling interfacial concentration improves printed film reproducibility and the fractional coverage of multicomponent films can be controlled to within a few percent. We first briefly review the important aspects of molecular ink diffusion at a stamp interface and how it relates to experimental duration. We then describe two examples that illustrate control over ink transfer during experiments: the role of contact time on monolayer reproducibility and molecular order, and the fine control of fractional monolayer coverage for the displacement printing of 1-adamantanethiolate SAMs by 1-dodecanethiol. PMID:24070334

Schwartz, Jeffrey J; Hohman, J Nathan; Morin, Elizabeth I; Weiss, Paul S

2013-10-14

92

A barrier-free molecular radical-molecule reaction:  

Microsoft Academic Search

The reaction of 3C2 (a3?) radical with O2 (X3?) molecule has been studied theoretically using ab initio Quantum Chemistry method. Both singlet and triplet potential energy surfaces (PES) are calculated at the CCSD(T)\\/aug-cc-pVDZ\\/\\/B3LYP\\/6-311+G(d)\\u000a + ZPE and G3B3 levels of theory. On the singlet PES of the title reaction, it is shown that the most feasible pathway should\\u000a be the O-atom

Ming-Hui Zuo; Ji-Lai Li; Xu-Ri Huang; Hui-Ling Liu; Cai-Yun Geng; Fei Li; Chia-Chung Sun

2007-01-01

93

Evidence on single-molecule transport in electrostatically-gated molecular transistors  

NASA Astrophysics Data System (ADS)

We show that, if adequately formulated for molecular electronics, the barrier picture can quantitatively reproduce the currents and describe the orbital gating in the molecular transistors fabricated by Song et al. [H. Song, Y. Kim, Y.H. Jang, H. Jeong, M.A. Reed, T. Lee, Nature 462 (2009) 1039]. Based on our results, we demonstrate (i) that the measured current represents the contribution of a single molecule, and (ii) the linear dependence of the molecular orbital energy offset ?g on the voltage Vt at the Fowler-Nordheim minimum, validating thereby the transition voltage spectroscopy for the gated single molecule devices of Song et al.

Bâldea, Ioan; Köppel, Horst

2012-03-01

94

SiGe quantum dot molecules grown on patterned Si (001) substrates  

SciTech Connect

SiGe quantum dot molecules (QDMs) grown on patterned Si (001) substrates by molecular beam epitaxy were studied. Experimental results showed that the density, the dimension, and the dimension distribution of the SiGe QDMs grown in the windows were dependent on the window size. When the thickness of the Si{sub 0.8}Ge{sub 0.2} film was 40 nm, QDMs only appeared in the unpatterned areas of the Si substrate and none could be found inside the windows of 6x6 {mu}m{sup 2} on the same substrate. However, when the thickness of Si{sub 0.8}Ge{sub 0.2} film was increased to 80 nm, QDMs appeared both inside the windows and in the unpatterned areas, and the density of QDMs was reduced with the decrease in the window size. We attribute these results to the different strain relaxations in different size windows, which are caused by the edge effect of the epitaxial film in the window. Based on these experimental results we discuss the formation and the size stability of the QDMs and conclude that the formation of the SiGe QDM originates from an intrinsic cause of the strain relief mechanism. This work also shows that by means of the edge induced strain relaxation of the epitaxial film in the window, it is possible to reveal the influence of the strain on some physical properties of the SiGe film without changing its Ge atomic fraction.

Yang Hongbin; Zhang Xiangjiu; Jiang Zuiming; Yang Xinju; Fan Yongliang [Surface Physics Laboratory (National Key Laboratory), Fudan University, Shanghai 200433 (China)

2008-08-15

95

Non-linear molecular pattern classification using molecular beacons with multiple targets.  

PubMed

In vitro pattern classification has been highlighted as an important future application of DNA computing. Previous work has demonstrated the feasibility of linear classifiers using DNA-based molecular computing. However, complex tasks require non-linear classification capability. Here we design a molecular beacon that can interact with multiple targets and experimentally shows that its fluorescent signals form a complex radial-basis function, enabling it to be used as a building block for non-linear molecular classification in vitro. The proposed method was successfully applied to solving artificial and real-world classification problems: XOR and microRNA expression patterns. PMID:23743339

Lee, In-Hee; Lee, Seung Hwan; Park, Tai Hyun; Zhang, Byoung-Tak

2013-06-01

96

Molecular dynamics study of water molecule diffusion in oil-paper insulation materials  

NASA Astrophysics Data System (ADS)

Moisture is an important factor that influences the safe operation of transformers. In this study, molecular dynamics was employed to investigate the diffusion behavior of water molecules in the oil-paper insulation materials of transformers. Two oil-cellulose models were built. In the first model, water molecules were initially distributed in oil, and in the second model, water molecules were distributed in cellulose. The non-bonding energies of interaction between water molecules and oil, and between water molecules and cellulose, were calculated by the Dreiding force field. The interaction energy was found to play a dominant role in influencing the equilibrium distribution of water molecules. The radial direction functions of water molecules toward oil and cellulose indicate that the hydrogen bonds between water molecules and cellulose are sufficiently strong to withstand the operating temperature of the transformer. Mean-square displacement analysis of water molecules diffusion suggests that water molecules initially distributed in oil showed anisotropic diffusion; they tended to diffuse toward cellulose. Water molecules initially distributed in cellulose diffused isotropically. This study provides a theoretical contribution for improvements in online monitoring of water in transformers, and for subsequent research on new insulation materials.

Liao, Rui-Jin; Zhu, Meng-Zhao; Yang, Li-Jun; Zhou, Xin; Gong, Chun-Yan

2011-03-01

97

Immunopathological Roles of Cytokines, Chemokines, Signaling Molecules, and Pattern-Recognition Receptors in Systemic Lupus Erythematosus  

PubMed Central

Systemic lupus erythematosus (SLE) is an autoimmune disease with unknown etiology affecting more than one million individuals each year. It is characterized by B- and T-cell hyperactivity and by defects in the clearance of apoptotic cells and immune complexes. Understanding the complex process involved and the interaction between various cytokines, chemokines, signaling molecules, and pattern-recognition receptors (PRRs) in the immune pathways will provide valuable information on the development of novel therapeutic targets for treating SLE. In this paper, we review the immunopathological roles of novel cytokines, chemokines, signaling molecules, PRRs, and their interactions in immunoregulatory networks and suggest how their disturbances may implicate pathological conditions in SLE.

Yu, Shui-Lian; Kuan, Woon-Pang; Wong, Chun-Kwok; Li, Edmund K.; Tam, Lai-Shan

2012-01-01

98

Molecular topology analysis of the differences between drugs, clinical candidate compounds, and bioactive molecules.  

PubMed

A new method to decompose molecules is proposed and used to analyze drugs, clinical candidate compounds and bioactive molecules. The method classifies a set of molecules into a few well-defined classes based on their molecular framework. It is then possible to use these classes to investigate differences between drugs, clinical candidates and bioactive molecules. The analysis shows that in comparison with clinical candidates and bioactive compounds, drugs have a higher fraction of compounds with only one ring system. This conclusion is still valid after correcting for lipophilicity (ClogP) and molecular size, as well as any potential protein target bias in the data sets. Furthermore the molecular bridge part of compounds in the drug set has on average fewer ring systems than molecules from the other sets. The ring system complexity (RSC) was also investigated and for most topological classes drugs have a lower RSC than the clinical candidates and bioactive molecules. Hence, this study highlights differences in topology between drugs, clinical candidate compounds and bioactive molecules. PMID:21077637

Chen, Hongming; Yang, Yidong; Engkvist, Ola

2010-11-15

99

Patterns of molecular motors that guide and sort filaments.  

PubMed

Molecular motors can be immobilized to transport filaments and loads that are attached to these filaments inside a nano-device. However, if motors are distributed uniformly over a flat surface, the motility is undirected, and the filaments move equally in all directions. For many applications it is important to control the direction in which the filaments move, and two strategies have been explored to achieve this: applying external forces and confining the filaments inside channels. In this article, we discuss a third strategy in which the topography of the sample remains flat, but the motors are distributed non-uniformly over the surface. Systems of filaments and patterned molecular motors were simulated using a stochastic engine that included Brownian motion and filament bending elasticity. Using an evolutionary algorithm, patterns were optimized for their capacity to precisely control the paths of the filaments. We identified patterns of motors that could either direct the filaments in a particular direction, or separate short and long filaments. These functionalities already exceed what has been achieved with confinement. The patterns are composed of one or two types of motors positioned in lines or along arcs and should be easy to manufacture. Finally, these patterns can be easily combined into larger designs, allowing one to precisely control the motion of microscopic objects inside a device. PMID:23038219

Rupp, Beat; Nédélec, François

2012-11-21

100

Application of DNQ-based microlithography to patterning bioactive molecules and cells  

NASA Astrophysics Data System (ADS)

Photochemically induced surface functionality manipulation of Diazo-Naphto-Quinone/novolak polymeric films was used for controlling the specificity of the attachment and growth of neuronal cells and biologically active molecules (proteins and peptides) patterning. Different microlithographic techniques (standard positive tone, negative tone image reversal based on catalyzed decarboxylation, positive tone of image reversal resist, and surface imaging based on silylation), controlling the surface hydrophobicity and surface concentration of carboxylic groups, were assessed in the view of the suitability as microlithographic techniques for patterning biologically active molecules and cells. It was found that DNQ-based materials and techniques can be easily transferred in bio-microlithography, which is the building of laterally ordered architectures with biological structural elements.

Nicolau, Dan V.; Taguchi, Takahisa; Taniguchi, Hiroshi; Yoshikawa, Susumu; Dusa, Mircea V.

1996-06-01

101

Dynamic expression patterns of ECM molecules in the developing mouse olfactory pathway.  

PubMed

Olfactory sensory neuron (OSN) axons follow stereotypic spatio-temporal paths in the establishment of the olfactory pathway. Extracellular matrix (ECM) molecules are expressed early in the developing pathway and are proposed to have a role in its initial establishment. During later embryonic development, OSNs sort out and target specific glomeruli to form precise, complex topographic projections. We hypothesized that ECM cues may help to establish this complex topography. The aim of this study was to characterize expression of ECM molecules during the period of glomerulogenesis, when synaptic contacts are forming. We examined expression of laminin-1, perlecan, tenascin-C, and CSPGs and found a coordinated pattern of expression of these cues in the pathway. These appear to restrict axons to the pathway while promoting axon outgrowth within. Thus, ECM molecules are present in dynamic spatio-temporal positions to affect OSN axons as they navigate to the olfactory bulb and establish synapses. PMID:18570250

Shay, Elaine L; Greer, Charles A; Treloar, Helen B

2008-07-01

102

Nucleosome-remodelling machines and other molecular motors observed at the single-molecule level.  

PubMed

Through its capability to transiently pack and unpack our genome, chromatin is a key player in the regulation of gene expression. Single-molecule approaches have recently complemented conventional biochemical and biophysical techniques to decipher the complex mechanisms ruling chromatin dynamics. Micromanipulations with tweezers (magnetic or optical) and imaging with molecular microscopy (electron or atomic force) have indeed provided opportunities to handle and visualize single molecules, and to measure the forces and torques produced by molecular motors, along with their effects on DNA or nucleosomal templates. By giving access to dynamic events that tend to be blurred in traditional biochemical bulk experiments, these techniques provide critical information regarding the mechanisms underlying the regulation of gene activation and deactivation by nucleosome and chromatin structural changes. This minireview describes some single-molecule approaches to the study of ATP-consuming molecular motors acting on DNA, with applications to the case of nucleosome-remodelling machines. PMID:21810177

Lavelle, Christophe; Praly, Elise; Bensimon, David; Le Cam, Eric; Croquette, Vincent

2011-09-08

103

Molecular wires in single-molecule junctions: charge transport and vibrational excitations.  

PubMed

We investigate the effect of vibrations on the electronic transport through single-molecule junctions, using the mechanically controlled break junction technique. The molecules under investigation are oligoyne chains with appropriate end groups, which represent both an ideally linear electrical wire and an ideal molecular vibrating string. Vibronic features can be detected as satellites to the electronic transitions, which are assigned to longitudinal modes of the string by comparison with density functional theory data. PMID:20521299

Ballmann, Stefan; Hieringer, Wolfgang; Secker, Daniel; Zheng, Qinglin; Gladysz, John A; Görling, Andreas; Weber, Heiko B

2010-07-12

104

Molecular Resolution Imaging of Protein Molecules in Liquid Using Frequency Modulation Atomic Force Microscopy  

NASA Astrophysics Data System (ADS)

We demonstrated molecular resolution imaging of biological samples such as bacteriorhodopsin protein molecules in purple membrane and isolated chaperonin (GroEL) protein molecules, both adsorbed on mica using frequency modulation atomic force microscope (FM-AFM) in liquid. We also showed that the frequency noise of FM-AFM in liquid can be greatly reduced by the reduction of the noise-equivalent deflection of an optical beam deflection sensor.

Yamada, Hirofumi; Kobayashi, Kei; Fukuma, Takeshi; Hirata, Yoshiki; Kajita, Teruyuki; Matsushige, Kazumi

2009-09-01

105

Millimeter-Wave Spectroscopic and Collisional Studies of Molecules and Molecular Ions  

NASA Astrophysics Data System (ADS)

Molecular spectroscopy in the millimeter- and submillimeter-wave regions is an important tool in molecular physics. Information on molecular motions and interactions is obtained from spectroscopic studies of energy levels and collisions. This information and the data from which it is derived are essential in remote sensing of the atmosphere and the interstellar medium. Remote sensing at submillimeter wavelengths is now possible, making higher frequency and quantum number measurements of known interstellar species like water, propionitrile and ethyl alcohol necessary. Remote sensing improvements have also facilitated the need for spectral data on suspected interstellar molecules like propylene. The desire to extract quantitative information from atmospheric remote sensing has resulted in the need for a better understanding of the molecular interactions that cause pressure broadening. The use of a cold molecular ion to magnify the effects of intermolecular interactions has serious implications for pressure broadening theory. The measurement and analysis of rotational spectra of the asymmetric rotors water and propionitrile and the internal rotors propylene and ethyl alcohol are presented. These investigations provide the data and analysis necessary for astronomical observation. The ethyl alcohol investigation is the first experimental millimeter-wave study of a molecule with an asymmetric internal rotor. This study provides the data necessary for detailed theoretical modeling of this type of problem. A novel new experimental technique for generating and studying molecular ions is presented. The first temperature dependent microwave pressure broadening study of a molecular ion colliding with a neutral molecule, HCO^{+} on H_2 , is presented.

Pearson, John Christoffersen

1995-01-01

106

Role of molecule flexibility on the nucleation of dislocations in molecular crystals  

NASA Astrophysics Data System (ADS)

We show that a molecule's flexibility described by changes to its conformation and orientation during deformation is vital for the proper representation of dislocation nucleation in molecular crystals. This is shown for the molecular crystal hexahydro-1,3,5-trinitro-s-triazine (RDX) by comparing direct atomistic simulations to two alternate forms of a continuum dislocation nucleation model for a crack tip loaded in pure shear. The atomistic simulations show the emission of partial dislocations. These are compared to continuum dislocation nucleation models based on generalized stacking fault (GSF) energy surfaces where the molecules are allowed to be either rigid or flexible. The rigid molecules are unable to represent the partial dislocations whereas the flexible molecules agree with the direct atomistic model to within 17% of the stress intensity factor for emission of the first partial dislocation and to within 1% for the second partial. This agreement first indicates that the molecule flexibility serves a critical role in the ductile behavior of the molecular crystal and, second, the continuum dislocation nucleation model represents the correct atomistic behavior, showing two partial dislocations connected by a stacking fault, when parameterized with GSF energy surfaces that account for the molecule flexibility.

Munday, Lynn B.; Mitchell, Robert L.; Knap, Jaroslaw; Chung, Peter W.

2013-10-01

107

Kinetics of hydrogen uptake by scavenger molecules - Insights from molecular modeling  

NASA Astrophysics Data System (ADS)

Mixed aromatic-alkyne molecules have been designed to scavenge and remove hydrogen in unwanted situations. Such materials in powdered solid form are mixed with catalytic metal particles that dissociate H 2 molecules into H radicals. However, many details of the H uptake mechanism remain poorly understood. Here we report molecular modeling studies, using both classical force fields and first-principles density functional theory, aimed at providing enhanced understanding of the uptake kinetics. Such insights are important in improving the H scavenging efficiency of the present and next-generation materials, as well as to provide molecular-scale interpretation of supporting experiments.

Maiti, A.; Dinh, L. N.; Baumann, T. F.; Maxwell, R. S.; Saab, A. P.

2009-06-01

108

Communication: Identification of the molecule-metal bonding geometries of molecular nanowires  

NASA Astrophysics Data System (ADS)

Molecular nanowires in which a single molecule bonds chemically to two metal electrodes and forms a stable electrically conducting bridge between them have been studied intensively for more than a decade. However, the experimental determination of the bonding geometry between the molecule and electrodes has remained elusive. Here we demonstrate by means of ab initio calculations that inelastic tunneling spectroscopy (IETS) can determine these geometries. We identify the bonding geometries at the gold-sulfur interfaces of propanedithiolate molecules bridging gold electrodes that give rise to the specific IETS signatures that were observed in recent experiments.

Demir, Firuz; Kirczenow, George

2011-03-01

109

Laser Field Alignment of Organic Molecules on Semiconductor Surfaces: Toward Ultrafast Molecular Switches  

NASA Astrophysics Data System (ADS)

An ultrafast, nanoscale molecular switch is proposed, based on extension of the concept of nonadiabatic alignment to surface-adsorbed molecules. The switch consists of a conjugated organic molecule adsorbed onto a semiconducting surface and placed near a scanning tunneling microscope tip. A low-frequency, polarized laser field is used to switch the system by orienting the molecule with the field polarization axis, enabling conductance through the junction. Enhancement and spatial localization of the incident field by the metallic tip allow operation at low intensities. The principles of nonadiabatic alignment lead to switch on and off time scales far below rotational time scales.

Reuter, Matthew G.; Sukharev, Maxim; Seideman, Tamar

2008-11-01

110

Molecular level studies on binding modes of labeling molecules with polyalanine peptides  

NASA Astrophysics Data System (ADS)

In this work, the binding modes of typical labeling molecules (thioflavin T (ThT), Congo red (CR) and copper(ii) phthalocyanine tetrasulfonic acid tetrasodium salt (PcCu(SO3Na)4)) on pentaalanine, which is a model peptide segment of amyloid peptides, have been resolved at the molecular level by using scanning tunneling microscopy (STM). In the STM images, ThT molecules are predominantly adsorbed parallel to the peptide strands and two binding modes could be identified. It was found that ThT molecules are preferentially binding on top of the peptide strand, and the mode of intercalated between neighboring peptides also exists. The parallel binding mode of CR molecules can be observed with pentaalanine peptides. Besides the binding modes of labeling molecules, the CR and PcCu(SO3Na)4 display different adsorption affinity with the pentaalanine peptides. The results could be beneficial for obtaining molecular level insight of the interactions between labeling molecules and peptides.In this work, the binding modes of typical labeling molecules (thioflavin T (ThT), Congo red (CR) and copper(ii) phthalocyanine tetrasulfonic acid tetrasodium salt (PcCu(SO3Na)4)) on pentaalanine, which is a model peptide segment of amyloid peptides, have been resolved at the molecular level by using scanning tunneling microscopy (STM). In the STM images, ThT molecules are predominantly adsorbed parallel to the peptide strands and two binding modes could be identified. It was found that ThT molecules are preferentially binding on top of the peptide strand, and the mode of intercalated between neighboring peptides also exists. The parallel binding mode of CR molecules can be observed with pentaalanine peptides. Besides the binding modes of labeling molecules, the CR and PcCu(SO3Na)4 display different adsorption affinity with the pentaalanine peptides. The results could be beneficial for obtaining molecular level insight of the interactions between labeling molecules and peptides. Electronic supplementary information (ESI) available. See DOI: 10.1039/c0nr00782j

Mao, Xiaobo; Wang, Chenxuan; Ma, Xiaojing; Zhang, Min; Liu, Lei; Zhang, Lan; Niu, Lin; Zeng, Qindao; Yang, Yanlian; Wang, Chen

2011-04-01

111

Laser Field Alignment of Organic Molecules on Semiconductor Surfaces: Toward Ultrafast Molecular Switches  

SciTech Connect

An ultrafast, nanoscale molecular switch is proposed, based on extension of the concept of nonadiabatic alignment to surface-adsorbed molecules. The switch consists of a conjugated organic molecule adsorbed onto a semiconducting surface and placed near a scanning tunneling microscope tip. A low-frequency, polarized laser field is used to switch the system by orienting the molecule with the field polarization axis, enabling conductance through the junction. Enhancement and spatial localization of the incident field by the metallic tip allow operation at low intensities. The principles of nonadiabatic alignment lead to switch on and off time scales far below rotational time scales.

Reuter, Matthew G.; Sukharev, Maxim; Seideman, Tamar [Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113 (United States)

2008-11-14

112

Extended orientational correlation study for molecular liquids containing distorted tetrahedral molecules: Application to methylene halides  

NASA Astrophysics Data System (ADS)

The method of Rey [Rey, J. Chem. Phys. 126, 164506 (2007)] for describing how molecules orient toward each other in systems with perfect tetrahedral molecules is extended to the case of distorted tetrahedral molecules of c2v symmetry by means of introducing 28 subgroups. Additionally, the original analysis developed for perfect tetrahedral molecules, based on six groups, is adapted for molecules with imperfect tetrahedral shape. Deriving orientational correlation functions have been complemented with detailed analyses of dipole-dipole correlations. This way, (up to now) the most complete structure determination can be carried out for such molecular systems. In the present work, these calculations have been applied for particle configurations resulting from reverse Monte Carlo computer modeling. These particle arrangements are fully consistent with structure factors from neutron and x-ray diffraction measurements. Here we present a complex structural study for methylene halide (chloride, bromide, and iodide) molecular liquids, as possibly the best representative examples. It has been found that the most frequent orientations of molecules are of the 2:2 type over the entire distance range in these liquids. Focusing on the short range orientation, neighboring molecules turn toward each other with there ``H,Y''-``H,Y'' (Y: Cl, Br, I) edges, apart from CH2Cl2 where the H,H-H,Cl arrangement is the most frequent. In general, the structure of methylene chloride appears to be different from the structure of the other two liquids.

Pothoczki, Szilvia; Temleitner, László; Pusztai, László

2010-04-01

113

Streching of (DNA\\/functional molecules) complex between electrodes towards DNA molecular wire  

Microsoft Academic Search

DNA\\/functional molecules such as (Ru(bpy)32+ complex, conducting polymer etc.) complex was prepared to study molecular structure and I-V characteristics towards DNA molecular wire. For example, Ru(bpy)32+ was associated with duplex of DNA by not only electrostatic interaction but also intercalation in the aqueous solution. Singlemolecular structure of DNA\\/Ru(bpy)32+ complex was analyzed with AFM. We found a network structure of DNA\\/Ru(bpy)32+

Norihisa Kobayashi; Makoto Nishizawa; Shintarou Inoue; Kazuki Nakamura

2009-01-01

114

Length-dependent conductance of molecular wires and contact resistance in metal-molecule-metal junctions.  

PubMed

Molecular wires are covalently bonded to gold electrodes--to form metal-molecule-metal junctions--by functionalizing each end with a -SH group. The conductance of a wide variety of molecular junctions is studied theoretically by using first-principles density functional theory (DFT) combined with the nonequilibrium Green's function (NEGF) formalism. Based on the chain-length-dependent conductance of the series of molecular wires, the attenuation factor beta is obtained and compared with the experimental data. The beta value is quantitatively correlated to the molecular HOMO-LUMO gap. Coupling between the metallic electrode and the molecular bridge plays an important role in electron transport. A contact resistance of 6.0+/-2.0 Kohms is obtained by extrapolating the molecular-bridge length to zero. This value is of the same magnitude as the quantum resistance. PMID:18512822

Liu, Hongmei; Wang, Nan; Zhao, Jianwei; Guo, Yan; Yin, Xing; Boey, Freddy Y C; Zhang, Hua

2008-07-14

115

Munc18-1 Protein Molecules Move between Membrane Molecular Depots Distinct from Vesicle Docking Sites*  

PubMed Central

Four evolutionarily conserved proteins are required for mammalian regulated exocytosis: three SNARE proteins, syntaxin, SNAP-25, and synaptobrevin, and the SM protein, Munc18-1. Here, using single-molecule imaging, we measured the spatial distribution of large cohorts of single Munc18-1 molecules correlated with the positions of single secretory vesicles in a functionally rescued Munc18-1-null cellular model. Munc18-1 molecules were nonrandomly distributed across the plasma membrane in a manner not directed by mode of interaction with syntaxin1, with a small mean number of molecules observed to reside under membrane resident vesicles. Surprisingly, we found that the majority of vesicles in fully secretion-competent cells had no Munc18-1 associated within distances relevant to plasma membrane-vesicle SNARE interactions. Live cell imaging of Munc18-1 molecule dynamics revealed that the density of Munc18-1 molecules at the plasma membrane anticorrelated with molecular speed, with single Munc18-1 molecules displaying directed motion between membrane hotspots enriched in syntaxin1a. Our findings demonstrate that Munc18-1 molecules move between membrane depots distinct from vesicle morphological docking sites.

Smyth, Annya M.; Yang, Lei; Martin, Kirsty J.; Hamilton, Charlotte; Lu, Weiping; Cousin, Michael A.; Rickman, Colin; Duncan, Rory R.

2013-01-01

116

Munc18-1 protein molecules move between membrane molecular depots distinct from vesicle docking sites.  

PubMed

Four evolutionarily conserved proteins are required for mammalian regulated exocytosis: three SNARE proteins, syntaxin, SNAP-25, and synaptobrevin, and the SM protein, Munc18-1. Here, using single-molecule imaging, we measured the spatial distribution of large cohorts of single Munc18-1 molecules correlated with the positions of single secretory vesicles in a functionally rescued Munc18-1-null cellular model. Munc18-1 molecules were nonrandomly distributed across the plasma membrane in a manner not directed by mode of interaction with syntaxin1, with a small mean number of molecules observed to reside under membrane resident vesicles. Surprisingly, we found that the majority of vesicles in fully secretion-competent cells had no Munc18-1 associated within distances relevant to plasma membrane-vesicle SNARE interactions. Live cell imaging of Munc18-1 molecule dynamics revealed that the density of Munc18-1 molecules at the plasma membrane anticorrelated with molecular speed, with single Munc18-1 molecules displaying directed motion between membrane hotspots enriched in syntaxin1a. Our findings demonstrate that Munc18-1 molecules move between membrane depots distinct from vesicle morphological docking sites. PMID:23223447

Smyth, Annya M; Yang, Lei; Martin, Kirsty J; Hamilton, Charlotte; Lu, Weiping; Cousin, Michael A; Rickman, Colin; Duncan, Rory R

2012-12-06

117

Resonance enhanced multiphoton ionization spectra of molecules and molecular fragments. Technical report, January 1990--December 1990  

SciTech Connect

The objective of our effort is to carry out theoretical studies of resonance enhanced multiphoton ionization processes in molecules and molecular fragments. These studies are designed to provide a quantitatively robust analysis and prediction of key spectral features of interest in several ongoing experimental studies and applications of this technique.

NONE

1997-07-01

118

Streching of (DNA/functional molecules) complex between electrodes towards DNA molecular wire  

NASA Astrophysics Data System (ADS)

DNA/functional molecules such as (Ru(bpy)32+ complex, conducting polymer etc.) complex was prepared to study molecular structure and I-V characteristics towards DNA molecular wire. For example, Ru(bpy)32+ was associated with duplex of DNA by not only electrostatic interaction but also intercalation in the aqueous solution. Singlemolecular structure of DNA/Ru(bpy)32+ complex was analyzed with AFM. We found a network structure of DNA/Ru(bpy)32+ complex on the mica substrate, which is similar to native DNA. The height of DNA/Ru(bpy)32+ complex on the mica substrate was ranging from 0.8 to 1.6 nm, which was higher than the naked DNA (0.5-1.0 nm). This indicates that single-molecular DNA/Ru(bpy)32+ complex also connects to each other to form network structure on a mica substrate. In order to stretch DNA complex between electrodes, we employed high frequency and high electric field stretching method proposed by Washizu et al. We stretched and immobilized DNA single molecules between a pair of electrodes and its structures were analyzed with AFM technique. The I-V characteristics of DNA single molecules between electrodes were improved by the association of functional molecules with DNA. The molecular structure and I-V characteristics of DNA complex were discussed.

Kobayashi, Norihisa; Nishizawa, Makoto; Inoue, Shintarou; Nakamura, Kazuki

2009-08-01

119

Atoms, Molecules and Photons: An Introduction to Atomic Molecular and Quantum Physics  

Microsoft Academic Search

This introduction to Atomic and Molecular Physics explains how our present model of atoms and molecules has been developed during the last two centuries by many experimental discoveries and from the theoretical side by the introduction of quantum physics to the adequate description of micro-particles. It illustrates the wave model of particles by many examples and shows the limits of

Wolfgang Demtröder

2006-01-01

120

Recognition of damage-associated molecular patterns related to nucleic acids during inflammation and vaccination  

PubMed Central

All mammalian cells are equipped with large numbers of sensors for protection from various sorts of invaders, who, in turn, are equipped with molecules containing pathogen-associated molecular patterns (PAMPs). Once these sensors recognize non-self antigens containing PAMPs, various physiological responses including inflammation are induced to eliminate the pathogens. However, the host sometimes suffers from chronic infection or continuous injuries, resulting in production of self-molecules containing damage-associated molecular patterns (DAMPs). DAMPs are also responsible for the elimination of pathogens, but promiscuous recognition of DAMPs through sensors against PAMPs has been reported. Accumulation of DAMPs leads to massive inflammation and continuous production of DAMPs; that is, a vicious circle leading to the development of autoimmune disease. From a vaccinological point of view, the accurate recognition of both PAMPs and DAMPs is important for vaccine immunogenicity, because vaccine adjuvants are composed of several PAMPs and/or DAMPs, which are also associated with severe adverse events after vaccination. Here, we review as the roles of PAMPs and DAMPs upon infection with pathogens or inflammation, and the sensors responsible for recognizing them, as well as their relationship with the development of autoimmune disease or the immunogenicity of vaccines.

Jounai, Nao; Kobiyama, Kouji; Takeshita, Fumihiko; Ishii, Ken J.

2012-01-01

121

Structure of the Large Molecule Distribution in the Taurus Molecular Cloud  

NASA Astrophysics Data System (ADS)

We present observations of the distribution of long carbon chain molecules in TMC-1. The molecular line intensities for three cyanopolyyne molecules HC_5N, HC_7N and HC_9N were observed in a 25' diameter region. The four molecular line transitions were observed towards TMC-1 using the Robert C. Byrd Green Bank Telescope (GBT). These observations were made simultaneously in the frequency range 12780 to 13540 MHz. The images show the emission is primarily in along a narrow ridge. We present images of the molecular line intensity as a function of position, and compare the locations of peak molecular emission. Near the location of peak line intensity, the emission is well fit by a Gaussian profile. We present the ratio of molecular line intensities for the three species. The angular distribution of the molecules is very similar. We interpret the similarity of structure in terms of the chemical age of regions of the cloud. In addition, if all goes well, we will also present first results form the GBT 18 to 26 GHz Focal Plane Array receiver.

Langston, Glen I.; Woolard, Kyle

2010-06-01

122

Development of label-free molecular beacons based on abasic site-binding fluorescence molecules.  

PubMed

Here we report on a class of label-free molecular beacons (MBs) based on a non-covalent interaction with abasic site (AP site)-binding fluorescence molecules. In contrast to conventional MBs that require the chemical labelling with fluorophores and quenchers, our MB simply contains the AP site in the stem moiety, so that a small molecule specifically binds to the AP site. This binding event is accompanied by a significant quenching of its fluorescence, and thus a closed state of the AP site-containing MB (APMB) shows almost no fluorescence. Upon hybridization with a complementary DNA, APMB undergoes a conformational change to take an open state, resulting in an effective fluorescence enhancement due to a release of the molecule from the AP site. These sensing functions of APMB are discussed with a view towards further development of gene detection chemistry based on DNA-binding small molecules. PMID:18776283

Sato, Yusuke; Nishizawa, Seiichi; Teramae, Norio

2008-01-01

123

Fabrication of a highly oriented line structure on an aluminum surface and the nanoscale patterning on the nanoscale structure using highly functional molecules  

SciTech Connect

The surface of an Al plate was treated with a combination of chemical and electrochemical processes for fabrication of surface nanoscale structures on Al plates. Chemical treatments by using acetone and pure water under supersonic waves were conducted on an Al surface. Additional electrochemical process in H{sub 2}SO{sub 4} solution created a finer and oriented nanoscale structure on the Al surface. Dynamic force microscopy (DFM) measurement clarified that the nanoscale highly oriented line structure was successfully created on the Al surface. The line distance was estimated approximately 30-40 nm. At the next stage, molecular patterning on the highly oriented line structure by functional molecules such as copper phthalocyanine (CuPc) and fullerene C{sub 60} was also conducted. CuPc or C{sub 60} molecules were deposited on the highly oriented line structure on Al. A toluene droplet containing CuPc molecules was cast on the nanostructured Al plate and was extended on the surface. CuPc or C{sub 60} deposition on the nanostructured Al surface proceeded by evaporation of toluene. DFM and x-ray photoemission spectroscopy measurements demonstrated that a unique molecular pattern was fabricated so that the highly oriented groove channels were filled with the functional molecules.

Watanabe, Y.; Kato, H.; Takemura, S.; Watanabe, H.; Hayakawa, K.; Kimura, S.; Okumura, D.; Sugiyama, T.; Hiramatsu, T.; Nanba, N.; Nishikawa, O.; Taniguchi, M. [Department of Electrical, Electronic and Information Engineering, College of Engineering, Kanto Gakuin University, 1-50-1 Mutsuurahigashi, Kanazawa-ku, Yokohama 236-8501 (Japan); Department of Biology and Chemistry, Kanazawa Institute of Technology, 7-1 Ohgigaoka, Nonoichi, Ishikawa 921-8501 (Japan)

2009-07-15

124

Interactions of liquid crystal-forming molecules with phospholipid bilayers studied by molecular dynamics simulations.  

PubMed

Recent experiments have shown that liquid crystals can be used to image mammalian cell membranes and to amplify structural reorganization in phospholipid-laden liquid crystal-aqueous interfaces. In this work, molecular dynamics simulations were employed to explore the interactions between commonly used liquid crystal-forming molecules and phospholipid bilayers. In particular, umbrella sampling was used to obtain the potential of mean force of 4-cyano-4'-pentylbiphenyl (5CB) and 4'-(3,4-difluor-phenyl)-4-pentyl-bicylohexyl (5CF) molecules partitioning into a dipalmitoylphosphatidylcholine bilayer. In addition, results of simulations are presented for systems consisting of a fully hydrated bilayer with 5CB or 5CF molecules at the lowest (4.5 mol %) and highest (20 mol %) concentrations used in recent laboratory experiments. It is found that mesogens preferentially partition from the aqueous phase into the membrane; the potential of mean force exhibits highly favorable free energy differences for partitioning (-18 k(B)T for 5CB and -26 k(B)T for 5CF). The location and orientation of mesogens associated with the most stable free energies in umbrella sampling simulations of dilute systems were found to be consistent with those observed in liquid-crystal-rich bilayers. It is found that the presence of mesogens in the bilayer enhances the order of lipid acyl tails, and changes the spatial and orientational arrangement of lipid headgroup atoms. These effects are more pronounced at higher liquid-crystal concentrations. In comparing the behavior of 5CB and 5CF, a stronger spatial correlation (i.e., possibly leading to aggregation) is observed between 5CB molecules within a bilayer than between 5CF molecules. Also, the range of molecular orientations and positions along the bilayer normal is larger for 5CB molecules. At the same time, 5CF molecules were found to bind more strongly to lipid headgroups, thereby slowing the lateral motion of lipid molecules. PMID:16113112

Kim, Evelina B; Lockwood, Nathan; Chopra, Manan; Guzmán, Orlando; Abbott, Nicholas L; de Pablo, Juan J

2005-08-19

125

Interactions of Liquid Crystal-Forming Molecules with Phospholipid Bilayers Studied by Molecular Dynamics Simulations  

PubMed Central

Recent experiments have shown that liquid crystals can be used to image mammalian cell membranes and to amplify structural reorganization in phospholipid-laden liquid crystal-aqueous interfaces. In this work, molecular dynamics simulations were employed to explore the interactions between commonly used liquid crystal-forming molecules and phospholipid bilayers. In particular, umbrella sampling was used to obtain the potential of mean force of 4-cyano-4?-pentylbiphenyl (5CB) and 4?-(3,4-difluor-phenyl)-4-pentyl-bicylohexyl (5CF) molecules partitioning into a dipalmitoylphosphatidylcholine bilayer. In addition, results of simulations are presented for systems consisting of a fully hydrated bilayer with 5CB or 5CF molecules at the lowest (4.5 mol %) and highest (20 mol %) concentrations used in recent laboratory experiments. It is found that mesogens preferentially partition from the aqueous phase into the membrane; the potential of mean force exhibits highly favorable free energy differences for partitioning (?18 kBT for 5CB and ?26 kBT for 5CF). The location and orientation of mesogens associated with the most stable free energies in umbrella sampling simulations of dilute systems were found to be consistent with those observed in liquid-crystal-rich bilayers. It is found that the presence of mesogens in the bilayer enhances the order of lipid acyl tails, and changes the spatial and orientational arrangement of lipid headgroup atoms. These effects are more pronounced at higher liquid-crystal concentrations. In comparing the behavior of 5CB and 5CF, a stronger spatial correlation (i.e., possibly leading to aggregation) is observed between 5CB molecules within a bilayer than between 5CF molecules. Also, the range of molecular orientations and positions along the bilayer normal is larger for 5CB molecules. At the same time, 5CF molecules were found to bind more strongly to lipid headgroups, thereby slowing the lateral motion of lipid molecules.

Kim, Evelina B.; Lockwood, Nathan; Chopra, Manan; Guzman, Orlando; Abbott, Nicholas L.; de Pablo, Juan J.

2005-01-01

126

Molecular pathways: coexpression of immune checkpoint molecules: signaling pathways and implications for cancer immunotherapy.  

PubMed

The expression of immune checkpoint molecules on T cells represents an important mechanism that the immune system uses to regulate responses to self-proteins. Checkpoint molecules include cytotoxic T lymphocyte antigen-4, programmed death-1, lymphocyte activation gene-3, T-cell immunoglobulin and mucin protein-3, and several others. Previous studies have identified individual roles for each of these molecules, but more recent data show that coexpression of checkpoint molecules occurs frequently on cancer-specific T cells as well as on pathogen-specific T cells in chronic infections. As the signaling pathways associated with each checkpoint molecule have not been fully elucidated, blocking multiple checkpoints with specific monoclonal antibodies results in improved outcomes in several chronic viral infections as well as in a wide array of preclinical models of cancer. Recent clinical data suggest similar effects in patients with metastatic melanoma. These findings support the concept that individual immune checkpoint molecules may function through nonoverlapping molecular mechanisms. Here, we review current data regarding immune checkpoint molecule signaling and coexpression, both in cancer and infectious disease, as well as the results of preclinical and clinical manipulations of checkpoint proteins. Clin Cancer Res; 19(18); 4917-24. ©2013 AACR. PMID:23868869

Nirschl, Christopher J; Drake, Charles G

2013-07-18

127

Middle molecules and small-molecular-weight proteins in ESRD: properties and strategies for their removal.  

PubMed

Molecular weight has traditionally been the parameter most commonly used to classify uremic toxins, with a value of approximately 500 Da frequently used as a demarcation point below which the molecular weights of small nitrogenous waste products fall. This toxin group, the most extensively studied from a clinical perspective, is characterized by a high degree of water solubility and the absence of protein binding. However, uremia is mediated by the retention of a plethora of other compounds having characteristics that differ significantly from those of the previously mentioned group. As opposed to the relative homogeneity of the nitrogenous metabolite class, other uremic toxins collectively are a very heterogeneous group, not only with respect to molecular weight but also other characteristics, such as protein binding and hydrophobicity. A recently proposed classification scheme by the European Uraemic Toxin Work Group subdivides the remainder of molecules into 2 categories: protein-bound solutes and middle molecules. For the latter group, the Work Group proposes a molecular weight range (500-60,000 Da) that incorporates many toxins identified since the original middle molecule hypothesis, for which the upper molecular weight limit was approximately 2,000 Da. In fact, low-molecular-weight peptides and proteins (LMWPs) comprise nearly the entire middle molecule category in the new scheme. The purpose of this article is to provide an overview of the middle molecule class of uremic toxins, with the focus on LMWPs. A brief review of LMWP metabolism under conditions of normal (and in a few cases, abnormal) renal function will be presented. The physical characteristics of several LMWPs will also be presented, including molecular weight, conformation, and charge. Specific LMWPs to be covered will include beta 2-microglobulin, complement proteins (C3a and Factor D), leptin, and proinflammatory cytokines. The article will also include a discussion of the treatment-related factors influencing dialytic removal of middle molecules. Once these factors, which include membrane characteristics, protein-membrane interactions, and solute removal mechanisms, are discussed, an overview of the different therapeutic strategies used to enhance clearance of these compounds is provided. PMID:14681858

Clark, William R; Winchester, James F

2003-10-01

128

Molecules, cancer, and the surgeon. A review of molecular biology and its implications for surgical oncology.  

PubMed Central

Interactions between molecules control intra- and intercellular physiology. Cancer is emerging as a disease in which individual molecules are either overproduced, mutated, expressed at inappropriate stages of development, or lost due to inheritance or aberrant mitotic division. The major players in this contest of cellular control are growth factors, growth factor receptors (GFRs), signal transducers, and dominant or suppressor/recessive oncogenes. The tumors most frequently removed by surgeons have been reported to have changes in one or another of these types of molecules. The concept of multistage carcinogenesis, whereby malignancy arises after a sequence of changes that are cumulative, and passed from progenitor to daughter cells, is also being defined as a sequence of molecular, genetic, and chromosomal alterations. Molecular antineoplastic therapy is in early stages of development at the laboratory bench. The future may see patients screened for cancer susceptibility, evaluated for adjuvant therapy, and chosen for particular treatment based on molecular analysis. The types of cancer operations and the scope of surgical resection may change as molecular techniques enhance oncologic treatment.

Arbeit, J M

1990-01-01

129

Imaging polyatomic molecules in three dimensions using molecular frame photoelectron angular distributions.  

PubMed

We demonstrate a method for determining the full three-dimensional molecular-frame photoelectron angular distribution in polyatomic molecules using methane as a prototype. Simultaneous double Auger decay and subsequent dissociation allow measurement of the initial momentum vectors of the ionic fragments and the photoelectron in coincidence, allowing full orientation by observing a three-ion decay pathway, (H+, H+, CH2(+)). We find the striking result that at low photoelectron energies the molecule is effectively imaged by the focusing of photoelectrons along bond directions. PMID:23003951

Williams, J B; Trevisan, C S; Schöffler, M S; Jahnke, T; Bocharova, I; Kim, H; Ulrich, B; Wallauer, R; Sturm, F; Rescigno, T N; Belkacem, A; Dörner, R; Weber, Th; McCurdy, C W; Landers, A L

2012-06-08

130

A virus-like molecule in the early stage of encoded molecular evolution  

NASA Astrophysics Data System (ADS)

The recent advances of the evolutionary molecular engineering revealed the effectiveness of bonding strategy for assignment of the phenotype to its genotype, which non-enveloped viruses such as simple bacteriophages adopt. On the other hand, cellular organisms adopt another kind of the strategy, namely the compartmentalzation of both genotype and phenotype molecules in a single compartment enclosed with a cell membrane. The simplest strategy is that adopted by ribozymes in the RNA world. A single molecule carries both genotype and its phenotype. Based on the definition of “virus”-type and “cell”-type of the assignment strategy, we propose a virus-early/cell-late model of the history of life.

Nemoto, Naoto; Yanagawa, Hiroshi; Husimi, Yuzuru

1996-10-01

131

Resonant multiphoton ionization spectra of molecules and molecular fragments. Annual technical report, October 1987--September 1988  

SciTech Connect

The objective of the research under this contract is to carry out studies of resonant enhanced multiphoton ionization (REMPI) processes in molecules. In the (n+1)-REMPI process of interest an atom or molecule in a specific initial state absorbs n photons making a transition to an intermediate state from which it is subsequently ionized by absorption of an additional photon. The studies are designed to provide a quantitatively robust analysis and prediction of key spectral features in several ongoing experimental studies and potentially practical applications of this technique. The specific problems of interest to the authors in these studied are (1) the vibrational distributions of ions that can be expected in REMPI of small molecules and molecular fragments with particular emphasis on their non-Franck-Condon behavior. Such non-Franck-Condon behavior introduces serious complications in the use of the technique for state-specific production of ions, e.g., O{sub 2}{sup +}({nu}) and OH{sup +}({nu}), and in the extraction of state populations from REMPI signals, (2) rotational distributions of ions that can be produced in various REMPI schemes and how these distributions can be tuned by choice of the resonant state and influenced by the molecular character of the photoelectron, and (3) the circular dichroism in photoelectron angular distributions, i.e., the difference in photoelectron angular distributions produced by right- and left-circularly polarized, and their use as a probe of molecular alignment. Here the author will summarize the progress that has been made to date in the studies of these features and applications of REMPI of molecules and molecular fragments. A significant feature of these studies, which will be explicitly assumed throughout the discussion below, is that they are carried out using quantitatively reliable molecular photoelectron orbitals.

NONE

1988-12-31

132

Conductivity in alkylamine/gold and alkanethiol/gold molecular junctions measured in molecule/nanoparticle/molecule bridges and conducting probe structures.  

PubMed

Charge transport through alkane monolayers on gold is measured as a function of molecule length in a controlled ambient using a metal/molecule/nanoparticle bridge structure and compared for both thiol and amine molecular end groups. The current through molecules with an amine/gold junction is observed to be more than a factor of 10 larger than that measured in similar molecules with thiol/gold linkages. Conducting probe atomic force microscopy is also used to characterize the same monolayer systems, and the results are quantitatively consistent with those found in the nanoparticle bridge geometry. Scaling of the current with contact area is used to estimate that approximately 100 molecules are probed in the nanoparticle bridge geometry. For both molecular end groups, the room-temperature conductivity at low bias as a function of molecule length shows a reasonable fit to models of coherent nonresonant charge tunneling. The different conductivity is ascribed to differences in charge transfer and wave function mixing at the metal/molecule contact, including possible effects of amine group oxidation and molecular conformation. For the amine/Au contact, the nitrogen lone pair interaction with the gold results in a hybrid wave function directed along the molecule bond axis, whereas the thiol/Au contact leads to a more localized wave function. PMID:17279744

Chu, Changwoong; Na, Jeong-Seok; Parsons, Gregory N

2007-02-06

133

Distribution patterns of small-molecule ligands in the protein universe and implications for origin of life and drug discovery  

PubMed Central

Background Extant life depends greatly on the binding of small molecules (such as ligands) with macromolecules (such as proteins), and one ligand can bind multiple proteins. However, little is known about the global patterns of ligand-protein mapping. Results By examining 2,186 well-defined small-molecule ligands and thousands of protein domains derived from a database of druggable binding sites, we show that a few ligands bind tens of protein domains or folds, whereas most ligands bind only one, which indicates that ligand-protein mapping follows a power law. Through assigning the protein-binding orders (early or late) for bio-ligands, we demonstrate that the preferential attachment principle still holds for the power-law relation between ligands and proteins. We also found that polar molecular surface area, H-bond acceptor counts, H-bond donor counts and partition coefficient are potential factors to discriminate ligands from ordinary molecules and to differentiate super ligands (shared by three or more folds) from others. Conclusion These findings have significant implications for evolution and drug discovery. First, the chronology of ligand-protein binding can be inferred by the power-law feature of ligand-protein mapping. Some nucleotide-containing ligands, such as ATP, ADP, GDP, NAD, FAD, dihydro-nicotinamide-adenine-dinucleotide phosphate (NDP), nicotinamide-adenine-dinucleotide phosphate (NAP), flavin mononucleotide (FMN) and AMP, are found to be the earliest cofactors bound to proteins, agreeing with the current understanding of evolutionary history. Second, the finding that about 30% of ligands are shared by two or more domains will help with drug discovery, such as in finding new functions from old drugs, developing promiscuous drugs and depending more on natural products.

Ji, Hong-Fang; Kong, De-Xin; Shen, Liang; Chen, Ling-Ling; Ma, Bin-Guang; Zhang, Hong-Yu

2007-01-01

134

Single-Molecule Spectroscopy: From 2K, to Molecular Motors, to Quantum Optics  

NASA Astrophysics Data System (ADS)

It has now been more than ten years since the first optical detection and spectroscopy of a single molecule in a solid (Phys. Rev. Lett. 62, 2535 (1989)). The interest in optical probing of individual molecules continues to expand, driven by the lifting of ensemble averaging to expose hidden heterogeneity and by the ability to acquire local information on structure and dynamics in complex systems in a weakly perturbative manner. The early years concentrated on studies of aromatic hydrocarbon molecules like pentacene in organic crystals like p-terphenyl at liquid helium temperatures. Physical effects observed included spectral diffusion, magnetic resonance of a single molecular spin, and single-molecule vibrational structure. In the mid-90's, much of the effort in the field moved to room temperature, which allowed explorations of a wide array of biomolecules such as green fluorescent protein, local concentration sensors, enzymes performing catalysis, and many others. For example, single-molecule polarization studies of the kinesin molecular motor can be performed by bifunctional attachment of a fluorophore to the protein. When attached to a microtubule, a striking increase in motor orientational flexibility occurs with ADP as the bound nucleotide, while for three other nucleotide states, the fluorophore is essentially fixed in orientation. This observation provides insight into the mechanism of kinesin stepping, and represents a case where new biological information has been obtained from a single-molecule optical experiment. Finally, in the area of quantum optics, the high stability of some aromatic hydrocarbons in crystals has allowed the creation of a novel room-temperature light source of single photons on demand based on a single-molecule emitter. For each pump pulse, one and only one photon is emitted with high probability, making this light source potentially useful for quantum optical communication systems.

Moerner, W. E.

2001-03-01

135

Vascular bed origin dictates flow pattern regulation of endothelial adhesion molecule expression.  

PubMed

Endothelial cell phenotypes markedly differ, depending upon function and vascular bed of origin. Differences might account for specific susceptibility to pathological conditions. As leukocyte adhesion to activated endothelium is the initiating event in a range of diseases, we compared the influence of vascular bed-specific flow patterns on adhesion molecule expression in human saphenous vein (HSVEC) and coronary artery endothelial cells (HCAEC). In vitro, immune cell attachment was increased 1.6-fold when tumor necrosis factor (TNF)-alpha-stimulated HSVEC were exposed to coronary artery flow in place of physiological venous flow and 1.9-fold higher compared with attachment to cytokine-stimulated HCAEC exposed to coronary artery flow. This was associated with increased concentrations of soluble E-selectin, VCAM-1, and ICAM-1 in supernatants of HSVEC exposed to coronary artery flow compared with HCAEC exposed to the same flow pattern. Venous and coronary artery flow both increased TNF-alpha-induced E-selectin and ICAM-1 expression on HSVEC, but only coronary artery flow increased VCAM-1 expression. In marked contrast to HSVEC, venous and coronary artery flow attenuated TNF-alpha-induced E-selectin and VCAM-1 expression on HCAEC, whereas coronary artery flow further induced ICAM-1 on cytokine-stimulated HCAEC. With the exception of cytokine-induced ICAM-1, adhesion molecule expression on HSVEC exposed to coronary artery flow exceeded expression on HCAEC. Thus ICAM-1 expression involves complex flow-dependent and -independent pathways with marked dissimilarities between the two endothelial cell types studied. Interestingly, Kruppel-like factor (KLF) 4 overexpression in HCAEC and HSVEC significantly reduced TNF-alpha-induced E-selectin and VCAM-1 expression in static conditions, while ICAM-1 expression remained constant. Furthermore, both flow patterns induced KLF2 and KLF4 expression in HCAEC and HSVEC. Venous and coronary artery flow differentially influence endothelial adhesion molecule and transcription factor expression, depending on the vascular bed of origin. Differences in adhesion molecule expression and subsequent immune cell adhesion between HSVEC and HCAEC may contribute to different susceptibility to pathological conditions. PMID:17209004

Methe, Heiko; Balcells, Mercedes; Alegret, Maria del Carmen; Santacana, Marina; Molins, Blanca; Hamik, Anne; Jain, Mukesh K; Edelman, Elazer R

2007-01-05

136

Reorientational relaxation of aromatic molecules in the molecular cavity of crystalline syndiotactic polystyrene studied by molecular dynamics simulation  

NASA Astrophysics Data System (ADS)

The reorientational motion of aromatic molecules, which are clathrated in the molecular cavity of the crystalline syndiotactic polystyrene ? form was investigated using a molecular dynamics simulation. The in-plane and out-of-plane reorientation of phenyl rings and the rotational motion of methyl groups were examined for the guest species: benzene, toluene, p-xylene, m-xylene, o-xylene, and mesitylene. The cavity structures, the host guest interactions, and the resultant effects on the reorientational dynamics of the guests were investigated in detail. The reorientational relaxation time obeyed the Arrhenius law over a wide temperature range. The relaxation time was found to be significantly affected by the difference in the molecular structure of the guests, as a consequence of the variety in the host guest interaction.

Tamai, Yoshinori; Tsujita, Yoshiharu; Fukuda, Mitsuhiro

2005-04-01

137

Structure of the Large Molecule Distribution in the Taurus Molecular Cloud  

NASA Astrophysics Data System (ADS)

We present observations of the distribution of long carbon chain molecules in TMC-1. The molecular line intensities for three cyanopolyyne molecules HC5N,HC7N and HC9N were observed in a 25' diameter region. The four molecular line transitions were observed towards TMC-1 using the Robert C. Byrd Green Bank Telescope (GBT). These observations were made simultaneously in the frequency range 12780 to 13540 MHz. The images show the emission is primarily in along a narrow ridge. We present images of the molecular line intensity as a function of position, and compare the locations of peak molecular emission. Near the location of peak line intensity, the emission is well fit by a Gaussian profile. We present the ratio of molecular line intensities for the three species. Given the consistency of structure and peak location, we conclude that these cyanopolyynes have nearly the same chemical age. In addition, if all goes well, we will also present first results form the GBT 18 to 26 GHz Focal Plane Array receiver.

Langston, Glen; Woolard, K.; Mennicke, C.

2010-05-01

138

Molecular Frame Photoemission: Probe of the Photoionization Dynamics for Molecules in the Gas Phase  

NASA Astrophysics Data System (ADS)

Molecular frame photoemission is a very sensitive probe of the photoionization (PI) dynamics of molecules. This paper reports a comparative study of non-resonant and resonant photoionization of D2 induced by VUV circularly polarized synchrotron radiation at SOLEIL at the level of the molecular frame photoelectron angular distributions (MFPADs). We use the vector correlation method which combines imaging and time-of-flight resolved electron-ion coincidence techniques, and a generalized formalism for the expression of the I(?, ?e, varphie) MFPADs, where ? is the orientation of the molecular axis with respect to the light quantization axis and (?e, varphie) the electron emission direction in the molecular frame. Selected MFPADs for a molecule aligned parallel or perpendicular to linearly polarized light, or perpendicular to the propagation axis of circularly polarized light, are presented for dissociative photoionization (DPI) of D2 at two photon excitation energies, h? = 19 eV, where direct PI is the only channel opened, and h? = 32.5 eV, i.e. in the region involving resonant excitation of Q1 and Q2 doubly excited state series. We discuss in particular the properties of the circular dichroism characterizing photoemission in the molecular frame for direct and resonant PI. In the latter case, a remarkable behavior is observed which may be attributed to the interference occurring between undistinguishable autoionization decay channels.

Dowek, D.; Picard, Y. J.; Billaud, P.; Elkharrat, C.; Houver, J. C.

2009-04-01

139

Variable contact gap single-molecule conductance determination for a series of conjugated molecular bridges  

NASA Astrophysics Data System (ADS)

It is now becoming clear that the characteristics of the whole junction are important in determining the conductance of single molecules bound between two metal contacts. This paper shows through measurements on a series of seven conjugated molecular bridges that contact separation is an important factor in determining the electrical response of the molecular junction. These data are obtained using the I(t) method developed by Haiss et al since the scanning tunnelling microscope tip to substrate separation can be controlled through choice of the set-point (I0) current and calibrated with current-distance curves and knowledge of the terminal to terminal length of the molecular wire. The contact gap separation dependence is interpreted as arising from tilting of these molecules in the junction and this model is underpinned by ab initio transport computations. In this respect we make the general observation that conductance increases rather dramatically at higher tilt angle away from the normal for conformationally rigid molecular wires and that this increase in conductance arises from increased electronic coupling between the molecular bridge and the gold contacts.

Haiss, Wolfgang; Wang, Changsheng; Jitchati, Rukkiat; Grace, Iain; Martín, Santiago; Batsanov, Andrei S.; Higgins, Simon J.; Bryce, Martin R.; Lambert, Colin J.; Jensen, Palle S.; Nichols, Richard J.

2008-09-01

140

Fundamental absorption frequency from quasi-classical direct ab initio molecular dynamics: diatomic molecule  

SciTech Connect

A new approach is proposed to extract the fundamental absorption frequency from classical molecular dynamics simulation in which the oscillator amplitude is specified by setting the total energy equal to the harmonic zero-point energy. This approach is applied to D2 molecule. The fundamental absorption frequency and the anharmonic constant of D2, obtained from the quasiclassical direct ab initio molecular dynamics simulation method with the full Configuration Interaction level of theory with the aug-cc-pVTZ basis set, compare well with the experimentally observed values.

Aida, Misako; Dupuis, Michel

2005-01-31

141

Reducing the Molecule-Substrate Coupling in C60-Based Nanostructures by Molecular Interactions  

NASA Astrophysics Data System (ADS)

Codeposition of C60 and the three-dimensional molecular hydrocarbon 1,3,5,7-tetraphenyladamantane (TPA) on Au(111) leads to the spontaneous formation of molecular nanostructures in which each fullerene is locked into a specific orientation by three surrounding TPA. Scanning tunneling spectroscopy shows that the electronic coupling of C60 with the surface is significantly reduced in these nanostructures, enhancing the free-molecule properties. As evidenced by density functional theory simulations, the nanostructures are stabilized by 18 local electrostatic forces between C60 and TPA, resulting in a lifting of the C60 cage from the surface.

Franke, K. J.; Schulze, G.; Henningsen, N.; Fernández-Torrente, I.; Pascual, J. I.; Zarwell, S.; Rück-Braun, K.; Cobian, M.; Lorente, N.

2008-01-01

142

Nonadiabatic molecular high-order harmonic generation from polar molecules: Spectral redshift  

SciTech Connect

Molecular high-order harmonic generation (MHOHG) from the polar diatomic molecule HeH{sup 2+} in short intense laser fields is studied numerically. Due to the nonadiabatic response of the molecular dipole to the rapid change of laser intensity, a spectral redshift is predicted in high-intensity and ultrashort laser pulses, contrary to the blueshift observed in the harmonics generated from atoms in long laser pulses. The MHOHG temporal structures are investigated by a wavelet time-frequency analysis, which shows that the enhanced excitation of localized long lifetime excited states shifts the harmonic generation spectrum in the falling part of short laser pulses, due to the presence of a permanent dipole moment, and thus is unique to polar molecules.

Bian Xuebin; Bandrauk, Andre D. [Departement de Chimie, Universite de Sherbrooke, Sherbrooke, Quebec, J1K 2R1 (Canada)

2011-04-15

143

Molecular quantum defect orbital study of the Stark effect in the H{sub 3} molecule  

SciTech Connect

Stark maps and the distribution of oscillator strengths within a Stark manifold in the H{sub 3} molecule have been calculated by diagonalization of the Hamiltonian matrix using a molecular quantum defect orbital (MQDO) basis set. Our perturbative treatment, in which only experimental quantum defects have been used and no fitting parameters are required, explicitly accounts for the coupling between the rotation of the molecular core and the Rydberg-electron motion. A pure Hund's case (d) has been adopted for all the Rydberg states except for the np series, for which Hund's case (b) is considered to be more realistic. A mixing of some of the np Stark states with those belonging to other Rydberg series appears to occur. The presently achieved results conform very well with other reliable theoretical values, in the absence of experimental data. The adequacy of the MQDO procedure for accurately dealing with properties related to the Stark effect in molecules is suggested.

Menendez, J. M.; Martin, I.; Velasco, A. M. [Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Valladolid, 47005 Valladolid (Spain)

2006-10-15

144

Dynamic decomposition of aliphatic molecules on Al(111) from ab initio molecular dynamics  

SciTech Connect

Ab initio molecular dynamics based on density functional theory within the generalized gradient approximation was used to explore decomposition on Al(111) of butanol-alcohol and butanoic-acid, two important boundary additives in Al processing. Each molecule was oriented with its functional group closest to the surface and then given an initial velocity toward the surface. Decomposition occurred upon collision with Al(111) resulting in the formation of adhered fragments that represent the very initial stages in additive film formation during plastic deformation where nascent Al is liberated. Bonding interactions over the simulation time frames were explored with contours of the electron localization function. Results of the simulations were compared with existing experimental studies of chemical decomposition on clean Al surfaces and found to be in qualitative accord. The effects of other initial molecular orientations on decomposition were explored in ancillary calculations where the molecules were rotated through 90 deg. and 180 deg. prior to collision with Al(111)

Zhong Jun; Hector, Louis G. Jr.; Adams, James B. [School of Materials, Arizona State University, Tempe, Arizona 85287-8706 (United States); Materials and Processes Laboratory, General Motor R and D Center, Warren, Michigan 48090-9055 (United States); School of Materials, Arizona State University, Tempe, Arizona 85287-8706 (United States)

2009-03-15

145

Molecular dynamics description of a layer of water molecules on a hydrophobic surface  

NASA Astrophysics Data System (ADS)

Static and dynamic properties of a layer of water molecules on top of a graphite surface are studied by means of molecular dynamics simulations. The water molecules are described by a simple point charge flexible model, and the graphite is taken to be a set of featureless parallel sheets separated 3.4 A in the z direction. Our results indicate that, even at the lower temperatures considered, the water layer is not flat, with some hydrogen atoms pointing perpendicularly to the surface plane. The O-H stretching frequencies are also different than those of bulk water, appearing a new peak in the simulated spectra at a frequency approximately 200 wave numbers higher than the main peak. This peak is associated with the presence of non-H-bonded molecules.

Gordillo, M. C.; Marti, J.

2002-08-01

146

Nonlinear optical constants of polymers from molecular hyperpolarizabilities of donor-acceptor molecules  

NASA Astrophysics Data System (ADS)

A mathematical analysis previously developed to solve the quadratic tensor equations that relate molecular hyperpolarizability and bulk medium nonlinear optical constants is applied to donor-acceptor polyene molecules. The focus is on mutual polarization of spatially organized collections of molecules, e.g., chromophore side chains in an optical polymer. The performance of the electrostatic model is first confirmed by comparison with MOPAC calculations of composite molecules containing a pair of chromophores, and then applied to linear polymer chains as well as lattices in two and three dimensions. An optimal chromophore packing density is determined to maximize the macroscopic susceptibilities of polymer materials of the type studied. This is lower than the density allowed by the structure of the polymer, because of the mutual depolarization of chromophores at high packing densities.

Verwoerd, W. S.

147

Femtosecond observation of benzyne intermediates in a molecular beam: Bergman rearrangement in the isolated molecule  

PubMed Central

In this communication, we report our femtosecond real-time observation of the dynamics for the three didehydrobenzene molecules (p-, m-, and o-benzyne) generated from 1,4-, 1,3-, and 1,2-dibromobenzene, respectively, in a molecular beam, by using femtosecond time-resolved mass spectrometry. The time required for the first and the second C-Br bond breakage is less than 100 fs; the benzyne molecules are produced within 100 fs and then decay with a lifetime of 400 ps or more. Density functional theory and high-level ab initio calculations are also reported herein to elucidate the energetics along the reaction path. We discuss the dynamics and possible reaction mechanisms for the disappearance of benzyne intermediates. Our effort focuses on the isolated molecule dynamics of the three isomers on the femtosecond time scale.

Diau, Eric W.-G.; Casanova, Joseph; Roberts, John D.; Zewail, Ahmed H.

2000-01-01

148

An ab initio molecular dynamics study on hydrogen bonds between water molecules  

NASA Astrophysics Data System (ADS)

The quantitative estimation of the total interaction energy of a molecular system containing hydrogen bonds (H bonds) depends largely on how to identify H bonding. The conventional geometric criteria of H bonding are simple and convenient in application, but a certain amount of non-H bonding cases are also identified as H bonding. In order to investigate the wrong identification, we carry out a systematic calculation on the interaction energy of two water molecules at various orientation angles and distances using ab initio molecular dynamics method with the dispersion correction for the Becke-Lee-Yang-Parr (BLYP) functionals. It is shown that, at many orientation angles and distances, the interaction energies of the two water molecules exceed the energy criterion of the H bond, but they are still identified as H-bonded by the conventional ``distance-angle'' criteria. It is found that in these non-H bonding cases the wrong identification is mainly caused by short-range interaction between the two neighbouring water molecules. We thus propose that, in addition to the conventional distance and angle criteria of H bonding, the distance dH...H between the two neighbouring hydrogen atoms of the two water molecules should also be taken as a criterion, and the distance rO...H between the hydrogen atom of the H-bond donor molecule and the oxygen atom of the acceptor molecule should be restricted by a lower limit. When dH...H and rO...H are small (e.g., dH...H < 2.0 A? and rO...H < 1.62 A?), the repulsion between the two neighbouring atoms increases the total energy of the two water molecules dramatically and apparently weakens the binding of the water dimer. A statistical analysis and comparison of the numbers of the H bonds identified by using different criteria have been conducted on a Car-Parrinello ab initio molecular dynamics simulation with dispersion correction for a system of 64 water molecules at near-ambient temperature. They show that the majority of the H-bonds counted by using the conventional criteria combined with the dH...H criterion and the restriction of rO...H match what is identified by the binding energy criteria (e.g., E <= -10 kJ/mol), while some of them still have a binding energy that exceeds the energy criterion, indicating that the complicated quantum effects in H bonding can only be described by the three geometric parameters to a certain extent.

Pan, Zhang; Chen, Jing; Lü, Gang; Geng, Yi-Zhao; Zhang, Hui; Ji, Qing

2012-04-01

149

An ab initio molecular dynamics study on hydrogen bonds between water molecules.  

PubMed

The quantitative estimation of the total interaction energy of a molecular system containing hydrogen bonds (H bonds) depends largely on how to identify H bonding. The conventional geometric criteria of H bonding are simple and convenient in application, but a certain amount of non-H bonding cases are also identified as H bonding. In order to investigate the wrong identification, we carry out a systematic calculation on the interaction energy of two water molecules at various orientation angles and distances using ab initio molecular dynamics method with the dispersion correction for the Becke-Lee-Yang-Parr (BLYP) functionals. It is shown that, at many orientation angles and distances, the interaction energies of the two water molecules exceed the energy criterion of the H bond, but they are still identified as H-bonded by the conventional "distance-angle" criteria. It is found that in these non-H bonding cases the wrong identification is mainly caused by short-range interaction between the two neighbouring water molecules. We thus propose that, in addition to the conventional distance and angle criteria of H bonding, the distance d(H···H) between the two neighbouring hydrogen atoms of the two water molecules should also be taken as a criterion, and the distance r(O···H) between the hydrogen atom of the H-bond donor molecule and the oxygen atom of the acceptor molecule should be restricted by a lower limit. When d(H···H) and r(O···H) are small (e.g., d(H···H) < 2.0 Å and r(O···H) < 1.62 Å), the repulsion between the two neighbouring atoms increases the total energy of the two water molecules dramatically and apparently weakens the binding of the water dimer. A statistical analysis and comparison of the numbers of the H bonds identified by using different criteria have been conducted on a Car-Parrinello ab initio molecular dynamics simulation with dispersion correction for a system of 64 water molecules at near-ambient temperature. They show that the majority of the H-bonds counted by using the conventional criteria combined with the d(H···H) criterion and the restriction of r(O···H) match what is identified by the binding energy criteria (e.g., E ? -10 kJ/mol), while some of them still have a binding energy that exceeds the energy criterion, indicating that the complicated quantum effects in H bonding can only be described by the three geometric parameters to a certain extent. PMID:22559488

Pan, Zhang; Chen, Jing; Lü, Gang; Geng, Yi-Zhao; Zhang, Hui; Ji, Qing

2012-04-28

150

Self-Consistent Relativistic Molecular Calculations of Superheavy Molecules: (110X)F6  

Microsoft Academic Search

Using new relativistic molecular calculations within the Dirac-Slater scheme it is now feasible to study theoretically molecules containing superheavy elements. This opens a new era for the prediction of the physics and chemistry of superheavy elements. As an example we present the results for (110X)F6, where it is shown that relativistic effects are nearly of the same order of magnitude

A. Rosén; B. Fricke; T. Morovic

1978-01-01

151

Molecular effects in the neutrino mass determination from beta-decay of the tritium molecule  

SciTech Connect

Molecular final state energies and transition probabilities have been computed for beta-decay of the tritium molecule. The results are of sufficient accuracy to make a determination of the electron neutrino rest mass with an error not exceeding a few tenths of an electron volt. Effects of approximate models of tritium beta-decay on the neutrino mass determination are discussed. 14 refs., 3 figs., 1 tab.

Fackler, O.; Jeziorski, B.; Kolos, W.; Szalewicz, K.; Monkhorst, H.J.; Mugge, M.

1986-03-01

152

Interactions of Liquid Crystal-Forming Molecules with Phospholipid Bilayers Studied by Molecular Dynamics Simulations  

Microsoft Academic Search

Recent experiments have shown that liquid crystals can be used to image mammalian cell membranes and to amplify structural reorganization in phospholipid-laden liquid crystal-aqueous interfaces. In this work, molecular dynamics simulations were employed to explore the interactions between commonly used liquid crystal-forming molecules and phospholipid bilayers. In particular, umbrella sampling was used to obtain the potential of mean force of

Evelina B. Kim; Nathan Lockwood; Manan Chopra; Orlando Guzmán; Nicholas L. Abbott; Juan J. de Pablo

2005-01-01

153

Density functional theory/molecular mechanics approach for electronic g-tensors of solvated molecules.  

PubMed

A general density functional theory/molecular mechanics approach for computation of electronic g-tensors of solvated molecules is presented. We apply the theory to the commonly studied di-tert-butyl nitroxide molecule, the simplest model compound for nitroxide spin labels, and explore the role of an aqueous environment and of various approximations for its treatment. It is found that successive improvements of the solvent shift of the g-tensor are obtained by going from the polarizable continuum model to discrete solvent models of various levels of sophistication. The study shows that an accurate parametrization of the electrostatic potential and polarizability of the solvent molecules in terms of distributed multipole expansions and anisotropic polarizabilities to a large degree relieves the need to explicitly include water molecules in the quantum region, which is the common case in density functional/continuum model approaches. It is also shown that the local dynamics of the solvent around the solute significantly influences the electronic g-tensor and should be included in benchmarking of exchange-correlation functionals for evaluation of solvent shifts of g-tensors. These findings can have important ramifications for the use of advanced hybrid density functional theory/molecular mechanics approaches for modeling spin labels in solvents, proteins, and membrane environments. PMID:21449574

Rinkevicius, Zilvinas; Murugan, N Arul; Kongsted, Jacob; Aidas, Kestutis; Steindal, Arnfinn Hykkerud; Agren, Hans

2011-03-30

154

Multi-terminal quantum transport through a single benzene molecule: Evidence of a molecular transistor  

NASA Astrophysics Data System (ADS)

We explore multi-terminal quantum transport through a benzene molecule threaded by an Aharonov-Bohm flux $\\phi$. A simple tight-binding model is used to describe the system and all the calculations are done based on the Green's function formalism. With a brief description of two-terminal quantum transport, we present a detailed study of three-terminal transport properties through the benzene molecule to reveal the actual mechanism of electron transport. Here we numerically compute the multi-terminal conductances, reflection probabilities and current-voltage characteristics in the aspects of molecular coupling strength and magnetic flux $\\phi$. Most significantly we observe that, the molecular system where the benzene molecule is attached to three terminals can be operated as a transistor, and we call it a molecular transistor. This aspect can be utilized in designing nano-electronic circuits and our investigation may provide a basic framework to study electron transport in any complicated multi-terminal quantum system.

Maiti, Santanu K.

2010-08-01

155

Damage-associated molecular patterns and their receptors in upper airway pathologies.  

PubMed

Inflammation of the nasal (rhinitis) and sinus mucosa (sinusitis) are prevalent medical conditions of the upper airways that are concurrent in many patients; hence the terminology "rhinosinusitis". The disease status is further defined to be "chronic" in case symptoms persist for more than 12 weeks without resolution. A diverse spectrum of external factors including viral and bacterial insults together with epithelial barrier malfunctions could be implicated in the chronicity of the inflammatory responses in chronic rhinosinusitis (CRS). However, despite massive research efforts in an attempt to unveil the pathophysiology, the exact reason for a lack of resolution still remains poorly understood. A novel set of molecules that could be implicated in sustaining the inflammatory reaction may be found within the host itself. Indeed, besides mediators of inflammation originating from outside, some endogenous intracellular and/or extracellular matrix (ECM) components from the host can be released into the extracellular space upon damage induced during the initial inflammatory reaction where they gain functions distinct from those during normal physiology. These "host-self" molecules are known to modulate inflammatory responses under pathological conditions, potentially preventing resolution and contributing to the development of chronic inflammation. These molecules are collectively classified as damage-associated molecular patterns (DAMPs). This review summarizes the current knowledge regarding DAMPs in upper airway pathologies, also covering those that were previously investigated for their intracellular and/or ECM functions often acting as an antimicrobial agent or implicated in tissue/cell homeostasis, and for which their function as a danger signaling molecule was not assessed. It is, however, of importance to assess these molecules again from a point of view as a DAMP in order to further unravel the pathogenesis of CRS. PMID:23673984

Van Crombruggen, Koen; Jacob, Fenila; Zhang, Nan; Bachert, Claus

2013-05-15

156

Building foundations for molecular electronics: Growth of organic molecules on alkali halides as prototypical insulating substrates  

NASA Astrophysics Data System (ADS)

The epitaxy and growth of a series of organic molecules deposited on insulating surfaces were investigated by noncontact atomic force microscopy (nc-AFM). The molecules studied, C60, 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA), 3,4,9,10-perylene tetracarboxlylic diimide (PTCDI), and copper (II) phthalocyanine (CuPc), were selected to investigate the effect of different molecular geometries, charge distributions and intermolecular interactions and as interesting candidates in molecular electronic applications. As it is known that the properties of molecules are influenced by their structural arrangements, an understanding of the interactions of molecules with substrates of interest as well as the dominant processes involved in growth are of great interest. Model insulating substrates KBr and NaCl were used for growth studies, due to the necessity of insulators in electrically isolating device regions. Dewetting processes were observed in several of these systems: C 60 on KBr and NaCl, PTCDA on NaCl and PTCDI on NaCl. The specific influences of de- wetting are discussed for each system, in particular the morphological impact of dewetting and the driving of dewetting by strained metastable monolayers. For C60 deposits, interesting branched structures are formed in the process of dewetting which are remarkably stable once formed, yet do not represent the equilibrium growth morphology. A determination of the large cell coincident epitaxy reveals a small, yet significant discrepancy between the observed overlayer and calculated stable adsorption sites indicating a dominance of the intermolecular interaction over the molecule---substrate interaction. For both PTCDA and PTCDI on NaCl, strained metastable monolayer epitaxies were observed giving rise to a transition in both interface structure and morphology: a dewetting transition. A comparison of the observed molecular scale structures and growth modalities is made in order to build a framework for understanding the prevalence of dewetting for molecules on ionic surfaces. Finally, in order to better understand the connection between molecular scale structures and interesting opto-electronic properties, the application of a hybrid-electrostatic characterization technique by nc-AFM is discussed. Using this technique, the opto-electrostatic response of three different PTCDA arrangements on a nanotemplated NaCl surface are shown to differ according to the degree of intermolecular interaction permitted by the structure.

Burke, Sarah A.

157

Single-molecule study of molecular mobility in the cytoplasm of Escherichia coli.  

PubMed

The cytoplasm of bacterial cells is filled with individual molecules and molecular complexes that rely on diffusion to bring them together for interaction. The mobility of molecules in the cytoplasm has been characterized by several techniques mainly using fluorescent probes and ensemble methods. In order to probe the microenvrionment inside the cytoplasm as viewed by an individual molecule, we have studied single green fluorescent proteins (GFPs) diffusing in the cytoplasm of Escherichia coli cells at observation at rates ranging from 60 to 1000 Hz. Over long times the diffusion shows confinement due to the geometry of the cells themselves. A simulation in model cells using the actual distribution of cell sizes found in the experiments describes accurately the experimental results as well as reveals a short time diffusion coefficient that agrees well with that determined by ensemble methods. Higher short time diffusion coefficients can be obtained by filling the simulated cell with small spheres modeling cytoplasmic molecules and, depending on the density of particles included in the modeled cytoplasm, can approach the diffusion coefficient of GFPs found in water. Thus, single-molecule tracking combined with analysis using simple simulation of Brownian motion is able to reveal the main contributors to the GFP mobility in the cytoplasm of E. coli. PMID:23005785

Lill, Yoriko; Kaserer, Wallace A; Newton, Salete M; Lill, Markus; Klebba, Phillip E; Ritchie, Ken

2012-08-09

158

Embryonic expression patterns of the neural cell adhesion molecule gene are regulated by homeodomain binding sites.  

PubMed Central

During development of the vertebrate nervous system, the neural cell adhesion molecule (N-CAM) is expressed in a defined spatiotemporal pattern. We have proposed that the expression of N-CAM is controlled, in part, by proteins encoded by homeobox genes. This hypothesis has been supported by previous in vitro experiments showing that products of homeobox genes can both bind to and transactivate the N-CAM promoter via two homeodomain binding sites, HBS-I and HBS-II. We have now tested the hypothesis that the N-CAM gene is a target of homeodomain proteins in vivo by using transgenic mice containing native and mutated N-CAM promoter constructs linked to a beta-galactosidase reporter gene. Segments of the 5' flanking region of the mouse N-CAM gene were sufficient to direct expression of the reporter gene in the central nervous system in a pattern consistent with that of the endogenous N-CAM gene. For example, at embryonic day (E) 11, beta-galactosidase staining was found in postmitotic neurons in dorsolateral and ventrolateral regions of the spinal cord; at E14.5, staining was seen in these neurons throughout the spinal cord. In contrast, mice carrying an N-CAM promoter-reporter construct with mutations in both homeodomain binding sites (HBS-I and HBS-II) showed altered expression patterns in the spinal cord. At E11, beta-galactosidase expression was seen in the ventrolateral spinal cord, but was absent in the dorsolateral areas, and at E 14.5, beta-galactosidase expression was no longer detected in any cells of the cord. Homeodomain binding sites found in the N-CAM promoter thus appear to be important in determining specific expression patterns of N-CAM along the dorsoventral axis in the developing spinal cord. These experiments suggest that the N-CAM gene is an in vivo target of homeobox gene products in vertebrates. Images Fig. 2

Wang, Y; Jones, F S; Krushel, L A; Edelman, G M

1996-01-01

159

Allele-specific behavior of molecular networks: understanding small-molecule drug response in yeast.  

PubMed

The study of systems genetics is changing the way the genetic and molecular basis of phenotypic variation, such as disease susceptibility and drug response, is being analyzed. Moreover, systems genetics aids in the translation of insights from systems biology into genetics. The use of systems genetics enables greater attention to be focused on the potential impact of genetic perturbations on the molecular states of networks that in turn affects complex traits. In this study, we developed models to detect allele-specific perturbations on interactions, in which a genetic locus with alternative alleles exerted a differing influence on an interaction. We utilized the models to investigate the dynamic behavior of an integrated molecular network undergoing genetic perturbations in yeast. Our results revealed the complexity of regulatory relationships between genetic loci and networks, in which different genetic loci perturb specific network modules. In addition, significant within-module functional coherence was found. We then used the network perturbation model to elucidate the underlying molecular mechanisms of individual differences in response to 100 diverse small molecule drugs. As a result, we identified sub-networks in the integrated network that responded to variations in DNA associated with response to diverse compounds and were significantly enriched for known drug targets. Literature mining results provided strong independent evidence for the effectiveness of these genetic perturbing networks in the elucidation of small-molecule responses in yeast. PMID:23308257

Zhang, Fan; Gao, Bo; Xu, Liangde; Li, Chunquan; Hao, Dapeng; Zhang, Shaojun; Zhou, Meng; Su, Fei; Chen, Xi; Zhi, Hui; Li, Xia

2013-01-04

160

Strong-field Photoionization of Sputtered Neutral Molecules for Molecular Depth Profiling  

PubMed Central

Molecular depth profiles of an organic thin film of guanine vapor deposited onto a Ag substrate are obtained using a 40 keV C60 cluster ion beam in conjunction with time-of-flight secondary ion mass spectrometric (ToF-SIMS) detection. Strong-field, femtosecond photoionization of intact guanine molecules is used to probe the neutral component of the profile for direct comparison with the secondary ion component. The ability to simultaneously acquire secondary ions and photoionized neutral molecules reveals new fundamental information about the factors that influence the properties of the depth profile. Results show that there is an increased ionization probability for protonated molecular ions within the first 10 nm due to the generation of free protons within the sample. Moreover, there is a 50% increase in fragment ion signal relative to steady state values 25 nm before reaching the guanine/Ag interface as a result of interfacial chemical damage accumulation. An altered layer thickness of 20 nm is observed as a consequence of ion beam induced chemical mixing. In general, we show that the neutral component of a molecular depth profile using the strong-field photoionization technique can be used to elucidate the effects of variations in ionization probability on the yield of molecular ions as well as to aid in obtaining accurate information about depth dependent chemical composition that cannot be extracted from TOF-SIMS data alone.

Willingham, D; Brenes, D. A.; Wucher, A

2009-01-01

161

Allele-Specific Behavior of Molecular Networks: Understanding Small-Molecule Drug Response in Yeast  

PubMed Central

The study of systems genetics is changing the way the genetic and molecular basis of phenotypic variation, such as disease susceptibility and drug response, is being analyzed. Moreover, systems genetics aids in the translation of insights from systems biology into genetics. The use of systems genetics enables greater attention to be focused on the potential impact of genetic perturbations on the molecular states of networks that in turn affects complex traits. In this study, we developed models to detect allele-specific perturbations on interactions, in which a genetic locus with alternative alleles exerted a differing influence on an interaction. We utilized the models to investigate the dynamic behavior of an integrated molecular network undergoing genetic perturbations in yeast. Our results revealed the complexity of regulatory relationships between genetic loci and networks, in which different genetic loci perturb specific network modules. In addition, significant within-module functional coherence was found. We then used the network perturbation model to elucidate the underlying molecular mechanisms of individual differences in response to 100 diverse small molecule drugs. As a result, we identified sub-networks in the integrated network that responded to variations in DNA associated with response to diverse compounds and were significantly enriched for known drug targets. Literature mining results provided strong independent evidence for the effectiveness of these genetic perturbing networks in the elucidation of small-molecule responses in yeast.

Li, Chunquan; Hao, Dapeng; Zhang, Shaojun; Zhou, Meng; Su, Fei; Chen, Xi; Zhi, Hui; Li, Xia

2013-01-01

162

Structure transition and swapping pattern of clathrate hydrates driven by external guest molecules.  

PubMed

We first report here that under strong surrounding gas of external CH4 guest molecules the sII and sH methane hydrates are structurally transformed to the crystalline framework of sI, leading to a favorable change of the lattice dimension of the host-guest networks. The high power decoupling 13C NMR and Raman spectroscopies were used to identify structure transitions of the mixed CH4 + C2H6 hydrates (sII) and hydrocarbons (methylcyclohexane, isopentane) + CH4 hydrates (sH). The present findings might be expected to provide rational evidences regarding the preponderant occurrence of naturally occurring sI methane hydrates in marine sediments. More importantly, we note that the unique and cage-specific swapping pattern of multiguests is expected to provide a new insight for better understanding the inclusion phenomena of clathrate materials. PMID:16984168

Yeon, Sun-Hwa; Seol, Jiwoong; Lee, Huen

2006-09-27

163

Affinity flow fractionation of cells via transient interactions with asymmetric molecular patterns  

NASA Astrophysics Data System (ADS)

Flow fractionation of cells using physical fields to achieve lateral displacement finds wide applications, but its extension to surface molecule-specific separation requires labeling. Here we demonstrate affinity flow fractionation (AFF) where weak, short-range interactions with asymmetric molecular patterns laterally displace cells in a continuous, label-free process. We show that AFF can directly draw neutrophils out of a continuously flowing stream of blood with an unprecedented 400,000-fold depletion of red blood cells, with the sorted cells being highly viable, unactivated, and functionally intact. The lack of background erythrocytes enabled the use of AFF for direct enumeration of neutrophils by a downstream detector, which could distinguish the activation state of neutrophils in blood. The compatibility of AFF with capillary microfluidics and its ability to directly separate cells with high purity and minimal sample preparation will facilitate the design of simple and portable devices for point-of-care diagnostics and quick, cost-effective laboratory analysis.

Bose, Suman; Singh, Rishi; Hanewich-Hollatz, Mikhail; Shen, Chong; Lee, Chia-Hua; Dorfman, David M.; Karp, Jeffrey M.; Karnik, Rohit

2013-07-01

164

Simplifying the conductance profiles of molecular junctions: the use of the trimethylsilylethynyl moiety as a molecule-gold contact.  

PubMed

Conductance across a metal|molecule|metal junction is strongly influenced by the molecule-substrate contacts, and for a given molecular structure, multiple conductance values are frequently observed and ascribed to distinct binding modes of the contact at each of the molecular termini. Conjugated molecules containing a trimethylsilylethynyl terminus, -C?CSiMe(3) give exclusively a single conductance value in I(s) measurements on gold substrates, the value of which is similar to that observed for the same molecular backbone with thiol and amine based contacting groups when bound to under-coordinated surface sites. PMID:23104441

Marqués-González, Santiago; Yufit, Dmitry S; Howard, Judith A K; Martín, Santiago; Osorio, Henrry M; García-Suárez, Víctor M; Nichols, Richard J; Higgins, Simon J; Cea, Pilar; Low, Paul J

2012-10-29

165

Molecular features determining different partitioning patterns of papain and bromelain in aqueous two-phase systems.  

PubMed

The partitioning patterns of papain (PAP) and bromelain (BR), two well-known cysteine-proteases, in polyethyleneglycol/sodium citrate aqueous two-phase systems (ATPSs) were determined. Polyethyleneglycols of different molecular weight (600, 1000, 2000, 4600 and 8000) were assayed. Thermodynamic characterization of partitioning process, spectroscopy measurements and computational calculations of protein surface properties were also carried out in order to explain their differential partitioning behavior. PAP was observed to be displaced to the salt-enriched phase in all the assayed systems with partition coefficients (KpPAP) values between 0.2 and 0.9, while BR exhibited a high affinity for the polymer phase in systems formed by PEGs of low molecular weight (600 and 1000) with partition coefficients (KpBR) values close to 3. KpBR values resulted higher than KpPAP in all the cases. This difference could be assigned neither to the charge nor to the size of the partitioned biomolecules since PAP and BR possess similar molecular weight (23,000) and isoelectric point (9.60). The presence of highly exposed tryptophans and positively charged residues (Lys, Arg and His) in BR molecule would be responsible for a charge transfer interaction between PEG and the protein and, therefore, the uneven distribution of BR in these systems. PMID:23831382

Rocha, Maria Victoria; Nerli, Bibiana Beatriz

2013-07-03

166

CSO Broadband Molecular Line Surveys II: Intial Correlation Analysis Results for Complex Organic Molecules  

NASA Astrophysics Data System (ADS)

As was presented in the previous talk, we have conducted 25 broadband line surveys of interstellar sources in the ?=1.3 mm band using the Caltech Submillimeter Observatory. Using the results from the spectral analysis of these observations, the influence of physical environment on molecular complexity can be examined. Our broader research goal is to improve astrochemical models to the point where accurate predictions of complex molecular inventory can be made based on the physical and chemical environment of a given source. The CSO observations include a statistically-significant sample of sources, cover a range of physical environments, and target selected frequency windows containing transitions from a set of known complex organic molecules. We are now analyzing these line surveys to search for correlations between the relative abundances of organic molecules and the physical properties of the source (i.e. temperature, density, mass, etc.), as well as correlations between sets of molecules. Here we present the results from the initial quantitative analysis of these surveys, as well as chemical trends that have been determiend. The implications of these results for astrochemical models will also be discussed.

Sanders, James L. Sanders, Iii; Radhuber, Mary L.; Laas, Jacob C.; Hays, Brian M.; Lis, Darek C.; Weaver, Susanna L. Widicus

2013-06-01

167

Structural distributions from single-molecule measurements as a tool for molecular mechanics  

PubMed Central

A mechanical view provides an attractive alternative for predicting the behavior of complex systems since it circumvents the resource-intensive requirements of atomistic models; however, it remains extremely challenging to characterize the mechanical responses of a system at the molecular level. Here, the structural distribution is proposed to be an effective means to extracting the molecular mechanical properties. End-to-end distance distributions for a series of short poly-L-proline peptides with the sequence PnCG3K-biotin (n = 8, 12, 15 and 24) were used to experimentally illustrate this new approach. High-resolution single-molecule Förster-type resonance energy transfer (FRET) experiments were carried out and the conformation-resolving power was characterized and discussed in the context of the conventional constant-time binning procedure for FRET data analysis. It was shown that the commonly adopted theoretical polymer models—including the worm-like chain, the freely jointed chain, and the self-avoiding chain—could not be distinguished by the averaged end-to-end distances, but could be ruled out using the molecular details gained by conformational distribution analysis because similar polymers of different sizes could respond to external forces differently. Specifically, by fitting the molecular conformational distribution to a semi-flexible polymer model, the effective persistence lengths for the series of short poly-L-proline peptides were found to be size-dependent with values of ~190 Å, ~67 Å, ~51 Å, and ~76 Å for n = 8, 12, 15, and 24, respectively. A comprehensive computational modeling was carried out to gain further insights for this surprising discovery. It was found that P8 exists as the extended all-trans isomaer whereas P12 and P15 predominantly contained one proline residue in the cis conformation. P24 exists as a mixture of one-cis (75%) and two-cis (25%) isomers where each isomer contributes to an experimentally resolvable conformational mode. This work demonstrates the resolving power of the distribution-based approach, and the capacity of integrating high-resolution single-molecule FRET experiments with molecular modeling to reveal detailed structural information about the conformation of molecules on the length scales relevant to the study of biological molecules.

Hanson, Jeffrey A.; Brokaw, Jason; Hayden, Carl C.; Chu, Jhih-Wei; Yang, Haw

2011-01-01

168

Exploring molecular motors and switches at the single-molecule level.  

PubMed

Single-molecule techniques have propelled an impressive number of biophysical studies during the last decade. From relatively simple video-microscopy techniques, to sophisticated manipulation and detection apparata, single-molecule techniques are capable of tracking the movements and the reaction trajectories of single enzymatic units. By observing microspheres attached to biomolecules it is possible to follow the motion of molecular motors, or to detect conformational "switching" induced by regulatory proteins. Micromanipulation tools like optical tweezers have been widely applied to understand the mechanisms of linear molecular motors, and have allowed the measurement of the elementary steps and the forces produced by several motor proteins, including myosin, kinesin, and dynein. New experimental assays based on magnetic or optical "wrenches," which are able to apply and detect torques on rotary motors and biopolymers, are opening new possibilities in this field. Here, established and emerging magneto-optical manipulation and video-tracking techniques are reviewed, in the perspective of single molecular motors and regulatory proteins studies. PMID:15630689

Capitanio, M; Vanzi, F; Broggio, C; Cicchi, R; Normanno, D; Romano, G; Sacconi, L; Pavone, F S

2004-11-01

169

Molecular dynamics simulations on aqueous two-phase systems - Single PEG-molecules in solution  

PubMed Central

Background Molecular Dynamics (MD) simulations are a promising tool to generate molecular understanding of processes related to the purification of proteins. Polyethylene glycols (PEG) of various length are commonly used in the production and purification of proteins. The molecular mechanisms behind PEG driven precipitation, aqueous two-phase formation or the effects of PEGylation are however still poorly understood. Results In this paper, we ran MD simulations of single PEG molecules of variable length in explicitly simulated water. The resulting structures are in good agreement with experimentally determined 3D structures of PEG. The increase in surface hydrophobicity of PEG of longer chain length could be explained on an atomic scale. PEG-water interactions as well as aqueous two-phase formation in the presence of PO4 were found to be correlated to PEG surface hydrophobicity. Conclusions We were able to show that the taken MD simulation approach is capable of generating both structural data as well as molecule descriptors in agreement with experimental data. Thus, we are confident of having a good in silico representation of PEG.

2012-01-01

170

Chemoinformatic Analysis of Combinatorial Libraries, Drugs, Natural Products and Molecular Libraries Small Molecule Repository  

PubMed Central

A multiple criteria approach is presented, that is used to perform a comparative analysis of four recently developed combinatorial libraries to drugs, Molecular Libraries Small Molecule Repository (MLSMR) and natural products. The compound databases were assessed in terms of physicochemical properties, scaffolds and fingerprints. The approach enables the analysis of property space coverage, degree of overlap between collections, scaffold and structural diversity and overall structural novelty. The degree of overlap between combinatorial libraries and drugs was assessed using the R-NN curve methodology, which measures the density of chemical space around a query molecule embedded in the chemical space of a target collection. The combinatorial libraries studied in this work exhibit scaffolds that were not observed in the drug, MLSMR and natural products collections. The fingerprint-based comparisons indicate that these combinatorial libraries are structurally different to current drugs. The R-NN curve methodology revealed that a proportion of molecules in the combinatorial libraries are located within the property space of the drugs. However, the R-NN analysis also showed that there are a significant number of molecules in several combinatorial libraries that are located in sparse regions of the drug space.

Singh, Narender; Guha, Rajarshi; Giulianotti, Marc; Pinilla, Clemencia; Houghten, Richard; Medina-Franco, Jose L.

2009-01-01

171

Molecular tailoring approach for geometry optimization of large molecules: Energy evaluation and parallelization strategies  

NASA Astrophysics Data System (ADS)

A linear-scaling scheme for estimating the electronic energy, gradients, and Hessian of a large molecule at ab initio level of theory based on fragment set cardinality is presented. With this proposition, a general, cardinality-guided molecular tailoring approach (CG-MTA) for ab initio geometry optimization of large molecules is implemented. The method employs energy gradients extracted from fragment wave functions, enabling computations otherwise impractical on PC hardware. Further, the method is readily amenable to large scale coarse-grain parallelization with minimal communication among nodes, resulting in a near-linear speedup. CG-MTA is applied for density-functional-theory-based geometry optimization of a variety of molecules including ?-tocopherol, taxol, ?-cyclodextrin, and two conformations of polyglycine. In the tests performed, energy and gradient estimates obtained from CG-MTA during optimization runs show an excellent agreement with those obtained from actual computation. Accuracy of the Hessian obtained employing CG-MTA provides good hope for the application of Hessian-based geometry optimization to large molecules.

Ganesh, V.; Dongare, Rameshwar K.; Balanarayan, P.; Gadre, Shridhar R.

2006-09-01

172

A molecular conveyor belt by controlled delivery of single molecules into ultrashort laser pulses  

NASA Astrophysics Data System (ADS)

Trapping and laser cooling in atomic physics enables control of single particles and their dynamics at the quantum level in a background-free environment. Ultrashort intense laser pulses reveal the ultimate control of electromagnetic fields, enabling the imaging of matter, in principle down to a single molecule or virus resolved on atomic scales. However, current methods fall short in overlapping each target with a pulse of comparable size. We combine the two fields by demonstrating a deterministic molecular conveyor, formed of electric trapping potentials. We deliver individual diatomic ions at millikelvin temperatures and with submicrometre positioning into few-femtosecond ultraviolet laser pulses. We initiate and probe the molecule's femtosecond dynamics and detect it and its response with 100% efficiency. This experiment might become key for investigations of individual molecules, such as structural determinations using few-femtosecond X-ray lasers. Our scheme may overlap each single molecule with a pulse, focused to (sub)micrometre size, providing the required number of photons at the repetition rate of the laser.

Kahra, Steffen; Leschhorn, Günther; Kowalewski, Markus; Schiffrin, Agustin; Bothschafter, Elisabeth; Fuß, Werner; de Vivie-Riedle, Regina; Ernstorfer, Ralph; Krausz, Ferenc; Kienberger, Reinhard; Schaetz, Tobias

2012-03-01

173

Novel method to estimate solubility of small molecules in cis-polyisoprene by molecular dynamics simulations  

NASA Astrophysics Data System (ADS)

A novel method to predict gas solubility in cis-1,4-polyisoprene is developed using molecular dynamics (MD) simulations under constant particle number, constant pressure and constant temperature (NPT) conditions. Analogous to the experimental sorption technique, the binary-phase model constructed of gas/polymer was prepared. In order to maintain external pressure of the whole system during long NPT-MD runs, the vapor phase was filled with virtual liquid which has no interaction with the gas molecules and has only a repulsive interaction with the polymer. After attaining equilibration of the system, the solubility of oxygen and carbon dioxide in the polymer phase were estimated in the temperature range from 273 K to 373 K by counting the number of gas molecules inside the polymer phase. The average solubility linearly increased with the increase in the external pressure, indicating that Henry's Law was satisfied. The solubility coefficient obtained from the present method showed good agreement with the experimental data. Concentration profiles of gas molecule showed that it was significantly higher near the interface than both in the gas phase and inside the polymer phase. The distinction between ``adsorbed'' and ``absorbed'' gas molecules and also their effect on the solubility was discussed.

Kikuchi, Hiroaki; Kuwajima, Satoru; Fukuda, Mitsuhiro

2001-10-01

174

Electrical properties of metal-molecule-silicon structures with varying molecular backbones, dipoles, and atomic tethers  

NASA Astrophysics Data System (ADS)

We present the results of an extensive experimental investigation of metal-monolayer-silicon junctions. By varying the molecular dipole, the molecular backbone, the Si-molecule linkage, and the Si-doping, we indentified critical features that determine the electrical transport and injection properties of the junctions. Two basic structures were used. One is an enclosed planar structure in which an organic monolayer is directly assembled on silicon and contacted with evaporated silver. The other was made via Flip Chip Lamination, a novel approach that relies on the formation of monolayers on a gold surface first, which enables the study of a wider range of molecular layers on silicon of very high-quality. Two charge transport regimes dominate: (1) a Schottky barrier limited regime where the molecular dipole results in silicon band bending at the junction interface, and (2) a tunneling regime where the molecular dipole creates a small local electric field that screens the electrical transport. Transition Voltage spectroscopy was used to identify electrical differences between ?-conjugated and alkyl backbones attributed to the extended ?-delocalization and variations due to the chemical nature of Si-atom linkage.

Richter, Curt A.; Gergel-Hackett, Nadine; Coll, Mariona; Hacker, Christina A.

2011-03-01

175

Distribution patterns of small-molecule ligands in the protein universe and implications for origin of life and drug discovery  

Microsoft Academic Search

BACKGROUND: Extant life depends greatly on the binding of small molecules (such as ligands) with macromolecules (such as proteins), and one ligand can bind multiple proteins. However, little is known about the global patterns of ligand-protein mapping. RESULTS: By examining 2,186 well-defined small-molecule ligands and thousands of protein domains derived from a database of druggable binding sites, we show that

Hong-Fang Ji; De-Xin Kong; Liang Shen; Ling-Ling Chen; Bin-Guang Ma; Hong-Yu Zhang

2007-01-01

176

Small Molecule Activators of the Heat Shock Response: Chemical Properties, Molecular Targets, and Therapeutic Promise  

PubMed Central

All cells have developed various mechanisms to respond and adapt to a variety of environmental challenges, including stresses that damage cellular proteins. One such response, the heat shock response (HSR), leads to the transcriptional activation of a family of molecular chaperone proteins that promote proper folding or clearance of damaged proteins within the cytosol. In addition to its role in protection against acute insults, the HSR also regulates lifespan and protects against protein misfolding that is associated with degenerative diseases of aging. As a result, identifying pharmacological regulators of the HSR has become an active area of research in recent years. Here, we review progress made in identifying small molecule activators of the HSR, what cellular targets these compounds interact with to drive response activation, and how such molecules may ultimately be employed to delay or reverse protein misfolding events that contribute to a number of diseases.

West, James D.; Wang, Yanyu; Morano, Kevin A.

2012-01-01

177

The quest for probiotic effector molecules--unraveling strain specificity at the molecular level.  

PubMed

Pharmaceutical agents are widely applied for the treatment of gastrointestinal (and systemic) disorders and their role as modulators of host cell responses is relatively well characterized. By contrast, we are only beginning to understand the molecular mechanisms by which health-promoting, probiotic bacteria act as host cell modulators. The last decade has seen a rapid development of the genomics field for the widely applied probiotic genus Lactobacillus, and nowadays dozens of full genome sequences are available, as well as sophisticated post genomic and genetic engineering tools. This development has enabled comparative (functional) genomics approaches to identify the bacterial effector molecules involved in molecular communication with the host system that may underlie the probiotic effects observed. These efforts can also be complemented with dedicated mutagenesis approaches to eliminate or alter these effector molecules, followed by assessment of the host interaction consequences thereof, allowing the elucidation of the molecular mechanisms involved in probiotic health effects. Many of these approaches have pinpointed that the Lactobacillus cell envelope contains several effector molecules that are pivotal in the direct signaling capacity of these bacteria that underlies their immunomodulatory effects, including lipoteichoic acid, peptidoglycan, and (glyco)proteins. Moreover, the cell envelope contains several compounds such as wall teichoic acid and capsular polysaccharides that may not be involved in direct signaling to the host cell, but still affect signaling through shielding of other bacterial effector molecules. Initial structural studies revealed subtle strain- and species-specific biochemical differences in the canonical cell envelope compounds that are involved in these host interactions. These biochemical variations include the degree and positioning of d-alanyl and glycosyl substitution in lipoteichoic acids, and acetylation of peptidoglycan. Furthermore, specific peptides derived from peptidoglycan and envelope associated (glyco)proteins were recently identified as potent immunomodulators. The latter findings are exciting in the light of the possibility of more pharmacological application of these bioactive probiotic molecules, and especially cost-effective production and targeted delivery of bioactive peptides seems to emerge as a feasible strategy to harness this knowledge. PMID:23059538

Lee, I-Chiao; Tomita, Satoru; Kleerebezem, Michiel; Bron, Peter A

2012-10-08

178

Attached molecular motor in a trapped single molecule assay as a bidimensional Brownian multistable system.  

PubMed

To elucidate the physical properties of the force generation mechanism in molecular motors, we have obtained an analytical solution of the bidimensional Fokker-Plank equation which describes a common setup used in single molecule experiments. As a first application of this general result, we have shown that the size of the trapping system affects the dwell time of a multistable particle linearly. A quantitative application to skeletal actomyosin complex, using direct observation of force generation dynamics in the literature, shows that the size of the trapping system used was important for increasing the dwell time of the myosin head stable states to an observable time scale. PMID:23848719

Marcucci, L; Yanagida, T

2013-06-24

179

Vibrational Excitation of Diatomic Molecular Ions in Strong Field Ionization of Diatomic Molecules  

SciTech Connect

A model based on the strong-field and Born-Oppenheimer approximations qualitatively describes the distribution over vibrational states formed in a diatomic molecular ion following ionization of the neutral molecule by intense laser pulses. Good agreement is found with a recent experiment [X. Urbain et al., Phys. Rev. Lett. 92, 163004 (2004)]. In particular, the observed deviation from a Franck-Condon-like distribution is reproduced. Additionally, we demonstrate control of the vibrational distribution by a variation of the peak intensity or a change of frequency of the laser pulse.

Kjeldsen, Thomas K.; Madsen, Lars Bojer [Department of Physics and Astronomy, University of Aarhus, 8000 Aarhus C (Denmark)

2005-08-12

180

Attached molecular motor in a trapped single molecule assay as a bidimensional Brownian multistable system  

NASA Astrophysics Data System (ADS)

To elucidate the physical properties of the force generation mechanism in molecular motors, we have obtained an analytical solution of the bidimensional Fokker-Plank equation which describes a common setup used in single molecule experiments. As a first application of this general result, we have shown that the size of the trapping system affects the dwell time of a multistable particle linearly. A quantitative application to skeletal actomyosin complex, using direct observation of force generation dynamics in the literature, shows that the size of the trapping system used was important for increasing the dwell time of the myosin head stable states to an observable time scale.

Marcucci, L.; Yanagida, T.

2013-06-01

181

Mitochondrial damage-associated molecular patterns activate ?? T-cells.  

PubMed

Gamma delta T-cells have been shown to be important in the early immunoinflammatory response to injury, which can be independent of infection. This sterile inflammatory response is believed to be, in part, associated with danger-associated molecular patterns (DAMPs). Mitochondrial DAMPs (MTDs) have been shown to be important in trauma-induced neutrophil activation, but it is unknown whether MTDs activate other innate immune cells, such as ?? T-cells. To study this, splenic CD3(+) ?? T-cells were isolated from ?? T-cell-deficient C57BL/6 mice and mitochondria isolated from wild type mouse livers. MTDs were isolated from mitochondria by sonication and centrifugation. Gamma delta T-cells were incubated with various concentrations of MTDs (0-500?µg/ml) for 24?h. T-cells were phenotyped for TLR expression by flow cytometry and the supernatants assayed for cytokine and growth factor content. MTDs caused a dose-dependent increase in TLR2 and TLR4 expression by ?? T-cells. Both the percentage of cells positive for TLRs and the degree of expression increased. MTDs also induced the production of IL-1?, IL-6, IL-10, RANTES, fibroblast growth factor-basic and vascular endothelial growth factor by ?? T-cells. These findings support the concept that the MTDs released after tissue/cellular injury are capable of activating ?? T-cells, thus initiating sterile inflammation, as well as subsequent healing processes. PMID:23757324

Schwacha, Martin G; Rani, Meenakshi; Zhang, Qiong; Nunez-Cantu, Oliver; Cap, Andre P

2013-06-11

182

Molecular dynamics of point mutated I-A(k) molecules expressed on lymphocytes.  

PubMed

We have recently reported the lateral and rotational diffusion parameters for I-A(k) molecules expressing various cytoplasmic truncations (Int. Immunol. 12 (2000) 1319). We now describe the membrane dynamics of I-A(k) with various mutations in the presumed contact region between alphabeta-heterodimers in an (alphabeta)2 dimer of dimers structure. Such mutations are known to strongly affect the antigen presentation ability of these molecules (Int. Immunol. 10 (1998) 1237-1249) but cause relatively small changes in the molecular dynamics of I-A(k). Lateral diffusion coefficients of I-A(k) wild-type molecules and mutants obtained via fringe fluorescence photobleaching recovery (FPR) ranged from 1.1 to 2.3x10(-10)cm2/s at room temperature while fractional mobilities averaged 75+/-6%. For all cell types examined, treatment with either hen egg lysozyme 46-61 peptide or db-cAMP reduced the I-A(k) mobile fraction by about 10% relative to untreated cells, suggesting that these treatments may increase lateral confinement of class II in lipid rafts or cytoskeletal interactions of the molecules. Wild-type I-A(k) and mutants capable of normal or partial antigen presentation exhibited, as a group, slightly longer rotational correlation times (RCT) at 4 degrees C than did mutants inactive in antigen presentation, 14+/-4 versus 10+/-1 micros, respectively. Moreover, peptide, cAMP and anti-CD40 mAb treatment all increased rotational correlation times for fully- and partially-functional I-A(k) but not for non-functional molecules. For example, 16 h peptide treatment yielded average RCTs of 28+/-12 and 10+/-1 micros for the groups of functional and non-functional molecules, respectively. Such modulation of the dynamics of functional class II molecules is consistent with these treatments' stabilization of class II or induction of new gene expression. Measurements of fluorescence resonant energy transfer between I-A(k), though complicated by cellular autofluorescence, averaged 6+/-7% over 15 cells or treatments, a result consistent with the presence of a small fraction of I-A(k) as a dimer of dimers species. In summary, our results suggest subtle changes in the molecular motions of class II molecules correlate with a significant impact on class II function. Molecules active in antigen presentation exhibit more restricted motion in the membrane, and thus presumably more extensive intermolecular interactions, than non-functional molecules. Further, treatments, such as db-cAMP and anti-CD40, which rescue antigen presentation by partially defective mutants, appear to increase such interactions, several types of which have already been reported for class II. A more detailed understanding of these phenomena will require both more sensitive biophysical tools and a more refined model of the role of class II intermolecular interactions in antigen presentation. PMID:11410253

Munnelly, H M; Brady, C J; Hagen, G M; Horvat, R D; Wade, W F; Roess, D A; Barisas, B G

2001-07-01

183

Analyzing different parameters of steered molecular dynamics for small membrane interacting molecules.  

PubMed

The aim of this report is two-fold: First, to show the applicability of the Steered Molecular Dynamics (SMD) methodology for analyzing non-specific interactions governing the membrane affinity process of small biological molecules. Second, to point out a correlation between the system response and certain combinations of the SMD parameters (spring-elastic-constant and pulling-group). For these purposes, a simplified membrane model was used, modeled as a non-polar region limited by two polar aqueous media in a continuous dielectric representation. Polarization-induced effects at both interfaces were taken into account by the "electrostatic images" method. To perform SMD simulations a harmonic external force, representing a spring acting on a selected atom, forces the molecule to "break" its interaction with the surrounding environment by extracting it out of the membrane. With this approach, small molecules and peptides, with known affinity for the membrane environment, were studied: the zwitterionic tryptophan residue and a pentapeptide AcWLKLL. The SMD parameters, spring-elastic-constant and pulling-group, were varied and combined in order to analyze the systems responses in each case. It was observed that, the spring stiffness was crucial to reveal specific events that occur during the molecule behavior; hence, it was directly responsible for the sensitivity of this methodology. The pulling-group selected highly influenced on the reaction pathway, a fact that it was not observed with other parameters; consequently, force profiles are like the "fingerprints" of these induced pathways. The potential profile for the tryptophan was recovered from the SMD simulations being in good agreement with that estimated by an approximation method. With this rather simple model approach, SMD methodology has proven to be suitable for revealing the main interactions that govern the membrane affinity processes of small molecules and peptides. PMID:16002307

Lorenzo, Alicia C; Bisch, Paulo M

2005-09-01

184

Anomalous water molecules and mechanistic effects of water nanotube clusters confined to molecular porous crystals.  

PubMed

The movement of water molecules in the limited space present within nanoscale regions, which is different from the molecular motion of bulk water, is significantly affected by strong interfacial interactions with the surrounding outer walls. Hence, most of the water molecules that are confined to nanochannel spaces having widths less than ca. 2 nm can generally be classified together as "structural water". Since the motions of such water molecules are limited by interfacial interactions with the outer wall, the nature of structural water, which is strongly influenced by the interactions, will have different characteristics from normal water. For our investigations on the characteristics of structural water, we have developed a nanoporous crystal with a diameter of ca. 1.6 nm; it was constructed from 1-D hydrophilic channels by self-organization of the designed molecules. A tubelike three-layered water cluster, called a water nanotube (WNT), is formed in each internal channel space and is regulated by H-bonds with the outer wall. The WNT undergoes a glass transition (T(g) = 107 K) and behaves as a liquid; it freezes at 234 K and changes into an icelike nanotube cluster. In this study, the structure of the WNT is investigated through neutron structure analysis, and it is observed to stabilize by a mechanistic anchor effect of structural water. Furthermore, from neutron-scattering experiments, it is seen that a few water molecules around the center of the WNT move approximately with the same diffusion constant as those in bulk water; however, the residence time and average jump length are longer, despite the restrictions imposed by the H-bonding with structural water. The behavior of mobile water within a WNT is investigated; this can be used to elucidate the mechanism for the effect of structural water on vital functions on the cell surface. PMID:20102158

Tadokoro, Makoto; Ohhara, Takashi; Ohhata, Yuhki; Suda, Takaaki; Miyasato, Yuji; Yamada, Takeshi; Kikuchi, Tatsuya; Tanaka, Ichiro; Kurihara, Kazuo; Oguni, Masaharu; Nakasuji, Kazuhiro; Yamamuro, Osamu; Ryota, Kuroki

2010-02-18

185

Direct observation of molecular orbitals in an individual single-molecule magnet Mn12 on Bi(111).  

PubMed

Single-molecule nanomagnets have unique quantum properties, and their potential applications require characterization and accessibility of individual single-molecule magnets on various substrates. We develop a gentle tip-deposition method to bring individual prototype single-molecule magnets, manganese-12-acetate (Mn12) molecules, onto the semimetallic Bi(111) surface without linker molecules, using low-temperature scanning tunneling microscopy. We are able to identify both the almost flat-lying and side-lying orientations of Mn12 molecules at 4.5 K. Energy-resolved spectroscopic mapping enables the first observation of several molecular orbitals of individual Mn12 molecules in real space, which is consistent with density functional theory calculations. Both experimental and theoretical results suggest that an energy gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of the almost flat-lying Mn12 is only 40% of such a gap for an isolated (free) Mn12 molecule, which is caused by charge transfer from the metallic surface states of Bi to the Mn12. Despite the reduction of this gap, STM images show that the local lattices of Bi(111) covered with Mn12 remain essentially intact, indicating that Mn12-Bi interactions are not strong. Our findings open an avenue to address directly the local structural and electronic properties of individual single-molecule magnets on solid substrates. PMID:23829481

Sun, Kai; Park, Kyungwha; Xie, Jiale; Luo, Jiyong; Yuan, Hongkuan; Xiong, Zuhong; Wang, Junzhong; Xue, Qikun

2013-07-11

186

MOLECULAR WEIGHT, ELECTROCHEMICAL AND BIOLOGICAL PROPERTIES OF TUBERCULIN PROTEIN AND POLYSACCHARIDE MOLECULES.  

PubMed

Studies have been made by means of sedimentation in the ultracentrifuge, and by diffusion and electrophoresis, to determine the molecular weights and homogeneity of the tuberculin protein and polysaccharide molecules as found in their natural state in the unchanged filtrates from culture media after growth of tubercle bacilli. These results have been compared with data obtained on fractions isolated by chemical procedures from them or from old tuberculin. By means of electrophoresis in the Tiselius apparatus it was possible to separate the protein from the polysaccharide, as these two fractions occur naturally in the original culture medium filtrates of acid-fast bacilli. The protein from the bovine strain of bacillus proved to be homogeneous in sedimentation (S(20) = 1.6), diffusion (D(20) = 12.0) and electrophoresis, with a molecular weight of about 10,000. The tuberculin polysaccharide isolated in electrophoresis appeared to be practically the same in sedimentation and in precipitin reaction as the polysaccharide isolated by chemical procedure. The latter proved to be homogeneous in sedimentation (S(20) = 1.6) and diffusion (D(20) = 11.0) with a molecular weight of about 9000. A practically homogeneous protein was isolated from the culture filtrate of the human tubercle bacillus H 37 by fractional ammonium sulfate precipitation, with a molecular weight of 32,000 (S(20) = 3.3; D(20) = 8.2). It was electrochemically homogeneous, with an isoelectric point at pH 4.3 and an isoionic point at pH 4.7. It could be dried or frozen with no loss in homogeneity. It was highly antigenic in the precipitin reaction and produced the anaphylactic type of local skin reaction in tuberculous guinea pigs, in contrast to the true tuberculin type of reaction caused by a purified PPD fraction. Furthermore death resulted in tuberculous guinea pigs from intracutaneous injection of exceptionally small amounts. A protein with molecular weight of about 17,000 was isolated from the filtrate from cultures of the timothy bacillus. The nucleic acid originally occurring in old tuberculin (OT) seems to be responsible for the high electrochemical mobility observed. From OT and the PPD made from it, potent but non-antigenic molecules of 16,000 and 9000 weight and with a low content of nucleic acid were isolated. With increase in size these deviated much from the normal compact spherical shape, and aggregation was evident from the tendency toward gel formation. The smallest molecule (9000) was homogeneous (S(20) = 1.0; D(20) = 10.0) and had lost some tuberculin potency. PMID:19870796

Seibert, F B; Pedersen, K O; Tiselius, A

1938-08-31

187

Signatures of the molecular potential in the ellipticity of high-order harmonics from aligned molecules  

NASA Astrophysics Data System (ADS)

We explore the information content of the polarization of high-order harmonics emitted from aligned molecules driven by a linearly polarized field. The study builds upon our previous work [Ramakrishna , Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.81.021802 81, 021802(R) (2010)], which illustrated that the phase of the continuum electronic wave function, and hence the underlying molecular potential, is responsible, at least in part, for the ellipticity observed in harmonic spectra. We use a simple model potential and systematically vary the potential parameters to investigate the sense in which, and the degree to which, the shape of the molecular potential is imprinted onto the polarization of the emitted harmonics. Strong ellipticity is observed over a wide range of potential parameters, suggesting that the emission of elliptically polarized harmonics is a general phenomenon, yet qualitatively determined by the molecular properties. The sensitivity of the ellipticity to the model parameters invites the use of ellipticity measurements as a probe of the continuum wave function and the underlying molecular potential.

Sherratt, Paul A. J.; Ramakrishna, S.; Seideman, Tamar

2011-05-01

188

LC-MS with electron ionization of cold molecules in supersonic molecular beams  

NASA Astrophysics Data System (ADS)

A new approach is described for the combination of electron ionization and LC-MS based on sample ionization as vibrationally cold molecules in a supersonic molecular beam (Cold EI). Cold EI of sample compounds in liquid solutions (methanol, acetonitrile, water, etc.) is achieved through spray formation, followed by soft thermal vaporization of the sample particles prior to their supersonic expansion and direct electron ionization of the sample compounds while they are contained in a supersonic molecular beam (SMB). Cold EI mass spectra were demonstrated to combine an enhanced molecular ion and improved mass spectral information (in comparison with standard EI), plus all the library searchable fragments. Cold EI enables the ionization of a broad range of compounds, including the full range of non-polar samples. Four orders of magnitude linear dynamic range is demonstrated and a detection limit of 2 pg was achieved for a 774 amu compound in single ion monitoring mode at m/z = 774. The method and apparatus are under continuous development and we feel that it can excel particularly in the analysis of unknown samples, while enabling fast LC-MS analysis through automated mass spectral deconvolution of coeluting LC peaks. In addition, the same MS system can also serve as an advanced GC-MS with supersonic molecular beams.

Granot, Ori; Amirav, Aviv

2005-06-01

189

Programmable nanoscale domain patterns in multilayers  

Microsoft Academic Search

The pattern formation in systems with multiple layers of adsorbate molecules is studied. We consider the presence of two types of molecules in each layer, which are characterized by different dipole moments. The patterns are characterized by the non-uniform distribution of the two molecules. A phase field model is developed to simulate the molecular motion and patterning under the combined

Wei Lu; David Salac

2005-01-01

190

Structure of the F-spondin Domain of Mindin an Integrin Ligand and Pattern Recognition Molecule  

SciTech Connect

Mindin (spondin-2) is an extracellular matrix protein of unknown structure that is required for efficient T-cell priming by dendritic cells. Additionally, mindin functions as a pattern recognition molecule for initiating innate immune responses. These dual functions are mediated by interactions with integrins and microbial pathogens, respectively. Mindin comprises an N-terminal F-spondin (FS) domain and C-terminal thrombospondin type 1 repeat (TSR). We determined the structure of the FS domain at 1.8-A resolution. The structure revealed an eight-stranded antiparallel beta-sandwich motif resembling that of membrane-targeting C2 domains, including a bound calcium ion. We demonstrated that the FS domain mediates integrin binding and identified the binding site by mutagenesis. The mindin FS domain therefore represents a new integrin ligand. We further showed that mindin recognizes lipopolysaccharide (LPS) through its TSR domain, and obtained evidence that C-mannosylation of the TSR influences LPS binding. Through these dual interactions, the FS and TSR domains of mindin promote activation of both adaptive and innate immune responses.

Y Li; C Cao; W Jia; L Yu; M Mo; Q Wang; Y Huang; J Lim; M Ishihara; et. al.

2011-12-31

191

Molecular architecture governs the kinetics of single molecule unfolding under force  

NASA Astrophysics Data System (ADS)

Proteins are a paradigm of complexity due to the broad energy scales involved in holding their folded structure intact under thermal fluctuations. Moreover, a subset of all proteins is known to withstand stretching forces on the order of 100 pN on the timescale of seconds. The dynamic mechanism by which these proteins support stress on the molecular level remains largely unknown. With the advent of single molecule techniques using the atomic force microscope (AFM), we measure the kinetics of unfolding as a function of a constant force for the archetypal mechanically stable proteins: the degradation protein ubiquitin and the 27th immunoglobulin domain (I27) in muscle. Instead of filtering the data, we develop a maximum likelihood method to analyze all force-clamp unfolding dwell times in order to deduce the underlying kinetics. We find that the large pool of data for both proteins is best fit with stretched exponential distributions, whose exponent depends on the molecular architecture of the protein. Our analysis of previously published kinetic data on ubiquitin as a function of force [PNAS, Garcia-Manyes et. al., 2009] follows stretched exponential kinetics at all forces. Rescaling the data by the exponent shows that the characteristic timescale for the rupture of the molecules increases slower than exponentially with the force, challenging the Bell model. The observed complex kinetics may therefore be of evolutionary importance, as it increases the protein's mechanical resilience. We discuss competing microscopic mechanisms by which the complex kinetic profiles may arise.

Brujic, Jasna

2010-03-01

192

The peptide-receptive transition state of MHC-1 molecules: Insight from structure and molecular dynamics  

SciTech Connect

MHC class I (MHC-I) proteins of the adaptive immune system require antigenic peptides for maintenance of mature conformation and immune function via specific recognition by MHC-I-restricted CD8(+) T lymphocytes. New MHC-I molecules in the endoplasmic reticulum are held by chaperones in a peptide-receptive (PR) transition state pending release by tightly binding peptides. In this study, we show, by crystallographic, docking, and molecular dynamics methods, dramatic movement of a hinged unit containing a conserved 3(10) helix that flips from an exposed 'open' position in the PR transition state to a 'closed' position with buried hydrophobic side chains in the peptide-loaded mature molecule. Crystallography of hinged unit residues 46-53 of murine H-2L(d) MHC-I H chain, complexed with mAb 64-3-7, demonstrates solvent exposure of these residues in the PR conformation. Docking and molecular dynamics predict how this segment moves to help form the A and B pockets crucial for the tight peptide binding needed for stability of the mature peptide-loaded conformation, chaperone dissociation, and Ag presentation.

Robinson H.; Mage, M.; Dolan, M.; Wang, R.; Boyd, L.; Revilleza, M.; Natarajan, K.; Myers, N.; Hansen, T.; Margulies, D.

2012-05-01

193

High energy sources and materials: High-temperature molecules and molecular energy storage  

NASA Astrophysics Data System (ADS)

The objective of this research was the characterization of molecular species which are important because of (a) their occurrence in high-temperature environments, as for example in the vapor over refractory solids, and in combustion, flames, and propellant burning; (b) their relevance to clarification and/or extension of the basic theory of molecular properties. The molecules studied were usually highly reactive or metastable and often inaccessible by the usual gas-phase spectroscopic methods. They were therefore trapped in a solid matrix, usually neon or orgon, at 4 K and investigated by optical and electron-spin-resonance (ESR) spectroscopies. This isolation procedure is known to produce only small perturbations and to yield information pertinent to the gas-phase species. The species studied included boron and bromine atoms, methylene radicals, diatomic boron, beryllium hydroxide, diatomic chlorine anion, carbonyl silene, diazasilene, the first-row transition-metal mono, di, and trifluorides and their corresponding hydrides and oxides, and a few rare-earth hydrides and fluorides. Vibrational frequencies, electronic transitions, g factors, spin-rotation constants, hyperfine coupling constants, zero-field-splittings, ground-state multiplicities, and perhaps some information about structure, were obtained. The molecules contained from one to seven unpaired electrons.

Weltner, W., Jr.

1980-10-01

194

Manipulating the motion of large molecules: Information from the molecular frame  

NASA Astrophysics Data System (ADS)

Large molecules have complex potential-energy surfaces with many local minima. They exhibit multiple stereoisomers, even at the low temperatures (˜1 K) in a molecular beam, with rich intra- and intermolecular dynamics. Over the last years, we have developed methods to manipulate the motion of large, complex molecules and to select their quantum states. We have exploited this state-selectivity, for example, to spatially separate individual structural isomers of complex molecules [1] and to demonstrate unprecedented degrees of laser alignment and mixed-field orientation of these molecules [2]. Such clean, well-defined samples strongly benefit, or simply allow, novel experiments on the dynamics of complex molecules, for instance, femtosecond pump-probe measurements, X-ray or electron diffraction of molecular ensembles (including diffraction-from-within experiments), or tomographic reconstructions of molecular orbitals. These samples could also be very advantageous for metrology applications, such as, for example, matter-wave interferometry or the search for electroweak interactions in chiral molecules. Moreover, they provide an extreme level of control for stereo-dynamically controlled reaction dynamics. We have recently exploited these state-selected and oriented samples to measure photoelectron angular distributions in the molecular frame (MFPADs) from non-resonant femtosecond-laser photoionization [3] and using the X-ray Free-Electron-Laser LCLS. We have also investigated X-ray diffraction imaging and, using ion momentum imaging, the induced radiation damage of these samples using the LCLS. This work was carried out within a collaboration for which J. Küpper, H. Chapman, and D. Rolles are spokespersons. The collaboration consists of CFEL (DESY, MPG, University Hamburg), Fritz-Haber-Institute Berlin, MPI Nuclear Physics Heidelberg, MPG Semi-conductor Lab, Aarhus University, FOM AMOLF Amsterdam, Lund University, MPI Medical Research Heidelberg, TU Berlin, Max Born Institute Berlin, and SLAC Menlo Park, CA, USA. The experiments were carried out using CAMP (designed and built by the MPG-ASG at CFEL) [4] at the LCLS (operated by Stanford University on behalf of the US DOE) [5]. [4pt] [1] Filsinger, Erlekam, von Helden, Küpper, Meijer, Phys. Rev. Lett. 100, 133003 (2008); Filsinger, Küpper, Meijer, Hansen, Maurer, Nielsen, Holmegaard, Stapelfeldt, Angew. Chem. Int. Ed. 48, 6900 (2009)[0pt] [2] Holmegaard, Nielsen, Nevo, Stapelfeldt, Filsinger, Küpper, Meijer, Phys. Rev. Lett. 102, 023001 (2009); Filsinger, Küpper, Meijer, Holmegaard, Nielsen, Nevo, Hansen, Stapelfeldt, J. Chem. Phys. 131, 064309, (2009); Nevo, Holmegaard, Nielsen, Hansen, Stapelfeldt, Filsinger, Meijer, Küpper, Phys. Chem. Chem. Phys. 11, 9912 (2009)[0pt] [3] Holmegaard, Hansen, Kalhøj, Kragh, Stapelfeldt, Filsinger, Küpper, Meijer, Dimitrovski, Abu-samha, Martiny, Madsen, Nature Phys. 6, 428 (2010)[0pt] [4] Strüder et al. Nucl Instrum Meth A 614, 483 (2010)[0pt] [5] Emma et al. Nat Photonics 4, 641 (2010)

Küpper, Jochen

2011-06-01

195

Molecular ions and protonated molecules observed in the atmospheric solids analysis probe analysis of steroids.  

PubMed

Atmospheric pressure chemical ionisation (APCI) has often been used to ionise steroids in mass spectrometry, usually when interfaced to high-performance liquid chromatography (HPLC). However, in positive ion mode, a dehydrated protonated molecule is often observed with a loss of structural information. The recently introduced technique of atmospheric solids analysis probe (ASAP) has the advantage that the sample can be analysed directly and does not need to be interfaced to HPLC. Existing ionisation sources such as direct analysis in real time (DART) and desorption electrospray ionisation (DESI) have shown the advantage of direct analysis techniques in a variety of applications. ASAP can be performed on commercial atmospheric pressure ionisation (API) mass spectrometers with only simple modifications to API sources. The samples are vaporised by hot nitrogen gas from the electrospray desolvation heater and ionised by a corona discharge. A range of commercially available steroids were analysed by ASAP to investigate the mechanism of ionisation. ASAP analysis of steroids generally results in the formation of the parent molecular ion as either the radical cation M+* or the protonated molecule MH+. The formation of the protonated molecule is a result of proton transfer from ionised water clusters in the source. However, if the source is dry, then formation of the radical cation is the primary ionisation mechanism. PMID:20212333

Ray, Andrew D; Hammond, Janet; Major, Hilary

2010-01-01

196

Small-molecule G-quadruplex interactions: Systematic exploration of conformational space using multiple molecular dynamics.  

PubMed

G-quadruplexes are higher-order four-stranded structures formed from repetitive guanine-containing tracts in nucleic acids. They comprise a core of stacked guanine-quartets linked by loops of length and sequence that vary with the context in which the quadruplex sequence occurs. Such sequences can be found in a number of genomic environments; at the telomeric ends of eukaryotic chromosomes, in promoter regions, in untranslated sequences and in open reading frames. Quadruplex formation can inhibit telomere maintenance, transcription and translation, especially when enhanced by quadruplex-binding small molecules, and quadruplex targeting is currently of considerable interest. The available experimental structural data shows that quadruplexes can have high conformational flexibility, especially in loop regions, which has hampered attempts to use high-throughput docking to find quadruplex-binding small-molecules with new scaffolds or to optimize existing ones with structure-based design methods. An approach to overcome the challenge of quadruplex conformational flexibility is presented here, which uses a combined multiple molecular dynamics and sampling approach. Two test small molecules have been used, RHPS4 and pyridostatin, which themselves have contrasting degrees of conformational flexibility. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 989-1005, 2013. PMID:23828641

Husby, Jarmila; Todd, Alan K; Platts, James A; Neidle, Stephen

2013-12-01

197

Nanomechanical recognition measurements of individual DNA molecules reveal epigenetic methylation patterns  

Microsoft Academic Search

Atomic force microscopy (AFM) is a powerful tool for analysing the shapes of individual molecules and the forces acting on them. AFM-based force spectroscopy provides insights into the structural and energetic dynamics of biomolecules by probing the interactions within individual molecules, or between a surface-bound molecule and a cantilever that carries a complementary binding partner. Here, we show that an

Rong Zhu; Stefan Howorka; Johannes Pröll; Ferry Kienberger; Johannes Preiner; Jan Hesse; Andreas Ebner; Vassili Ph. Pastushenko; Hermann J. Gruber; Peter Hinterdorfer

2010-01-01

198

Lack of the pattern recognition molecule mannose-binding lectin increases susceptibility to influenza A virus infection  

Microsoft Academic Search

BACKGROUND: Mannose-binding lectin (MBL), a pattern recognition innate immune molecule, inhibits influenza A virus infection in vitro. MBL deficiency due to gene polymorphism in humans has been associated with infection susceptibility. These clinical observations were confirmed by animal model studies, in which mice genetically lacking MBL were susceptible to certain pathogens, including herpes simplex virus 2. RESULTS: We demonstrate that

Wei-Chuan Chang; Mitchell R White; Patience Moyo; Sheree McClear; Steffen Thiel; Kevan L Hartshorn; Kazue Takahashi

2010-01-01

199

Nontypable Haemophilus influenzae Displays a Prevalent Surface Structure Molecular Pattern in Clinical Isolates  

PubMed Central

Non-typable Haemophilus influenzae (NTHi) is a Gram negative pathogen that causes acute respiratory infections and is associated with the progression of chronic respiratory diseases. Previous studies have established the existence of a remarkable genetic variability among NTHi strains. In this study we show that, in spite of a high level of genetic heterogeneity, NTHi clinical isolates display a prevalent molecular feature, which could confer fitness during infectious processes. A total of 111 non-isogenic NTHi strains from an identical number of patients, isolated in two distinct geographical locations in the same period of time, were used to analyse nine genes encoding bacterial surface molecules, and revealed the existence of one highly prevalent molecular pattern (lgtF+, lic2A+, lic1D+, lic3A+, lic3B+, siaA?, lic2C+, ompP5+, oapA+) displayed by 94.6% of isolates. Such a genetic profile was associated with a higher bacterial resistance to serum mediated killing and enhanced adherence to human respiratory epithelial cells.

Mauro, Silvia; Hood, Derek W.; Viadas, Cristina; Calatayud, Laura; Morey, Pau; Servin, Alain; Linares, Josefina; Oliver, Antonio; Bengoechea, Jose Antonio; Garmendia, Junkal

2011-01-01

200

Structural basis of recognition of pathogen-associated molecular patterns and inhibition of proinflammatory cytokines by camel peptidoglycan recognition protein.  

PubMed

Peptidoglycan recognition proteins (PGRPs) are involved in the recognition of pathogen-associated molecular patterns. The well known pathogen-associated molecular patterns include LPS from Gram-negative bacteria and lipoteichoic acid (LTA) from Gram-positive bacteria. In this work, the crystal structures of two complexes of the short form of camel PGRP (CPGRP-S) with LPS and LTA determined at 1.7- and 2.1-Å resolutions, respectively, are reported. Both compounds were held firmly inside the complex formed with four CPGRP-S molecules designated A, B, C, and D. The binding cleft is located at the interface of molecules C and D, which is extendable to the interface of molecules A and C. The interface of molecules A and B is tightly packed, whereas that of molecules B and D forms a wide channel. The hydrophilic moieties of these compounds occupy a common region, whereas hydrophobic chains interact with distinct regions in the binding site. The binding studies showed that CPGRP-S binds to LPS and LTA with affinities of 1.6 × 10(-9) and 2.4 × 10(-8) M, respectively. The flow cytometric studies showed that both LPS- and LTA-induced expression of the proinflammatory cytokines TNF-? and IL-6 was inhibited by CPGRP-S. The results of animal studies using mouse models indicated that both LPS- and LTA-induced mortality rates decreased drastically when CPGRP-S was administered. The recognition of both LPS and LTA, their high binding affinities for CPGRP-S, the significant decrease in the production of LPS- and LTA-induced TNF-? and IL-6, and the drastic reduction in the mortality rates in mice by CPGRP-S indicate its useful properties as an antibiotic agent. PMID:21454594

Sharma, Pradeep; Dube, Divya; Singh, Amar; Mishra, Biswajit; Singh, Nagendra; Sinha, Mau; Dey, Sharmistha; Kaur, Punit; Mitra, Dipendra K; Sharma, Sujata; Singh, Tej P

2011-03-21

201

Body-fixed relativistic molecular Hamiltonian and its application to nuclear spin-rotation tensor: linear molecules.  

PubMed

The relativistic molecular Hamiltonian written in the body-fixed frame of reference is the basis for high-precision calculations of spectroscopic parameters involving nuclear vibrations and/or rotations. Such a Hamiltonian that describes electrons fully relativistically and nuclei quasi-relativistically is just developed for semi-rigid nonlinear molecules [Y. Xiao and W. Liu, J. Chem. Phys. 138, 134104 (2013)]. Yet, the formulation should somewhat be revised for linear molecules thanks to some unusual features arising from the redundancy of the rotation around the molecular axis. Nonetheless, the resulting isomorphic Hamiltonian is rather similar to that for nonlinear molecules. Consequently, the relativistic formulation of nuclear spin-rotation (NSR) tensor for linear molecules is very much the same as that for nonlinear molecules. So is the relativistic mapping between experimental NSR and NMR. PMID:23883016

Xiao, Yunlong; Liu, Wenjian

2013-07-21

202

Body-fixed relativistic molecular Hamiltonian and its application to nuclear spin-rotation tensor: Linear molecules  

NASA Astrophysics Data System (ADS)

The relativistic molecular Hamiltonian written in the body-fixed frame of reference is the basis for high-precision calculations of spectroscopic parameters involving nuclear vibrations and/or rotations. Such a Hamiltonian that describes electrons fully relativistically and nuclei quasi-relativistically is just developed for semi-rigid nonlinear molecules [Y. Xiao and W. Liu, J. Chem. Phys. 138, 134104 (2013)]. Yet, the formulation should somewhat be revised for linear molecules thanks to some unusual features arising from the redundancy of the rotation around the molecular axis. Nonetheless, the resulting isomorphic Hamiltonian is rather similar to that for nonlinear molecules. Consequently, the relativistic formulation of nuclear spin-rotation (NSR) tensor for linear molecules is very much the same as that for nonlinear molecules. So is the relativistic mapping between experimental NSR and NMR.

Xiao, Yunlong; Liu, Wenjian

2013-07-01

203

Dressed-bound-state molecular strong-field approximation: Application to above-threshold ionization of heteronuclear diatomic molecules  

SciTech Connect

The molecular strong-field approximation (MSFA), which includes dressing of the molecular bound state, is introduced and applied to above-threshold ionization of heteronuclear diatomic molecules. Expressions for the laser-induced molecular dipole and polarizability as functions of the laser parameters (intensity and frequency) and molecular parameters [molecular orientation, dipole, and parallel and perpendicular polarizabilities of the highest occupied molecular orbital (HOMO)] are presented. Our previous MSFA theory, which incorporates the rescattering effects, is generalized from homonuclear to heteronuclear diatomic molecules. Angle- and energy-resolved high-order above-threshold ionization spectra of oriented heteronuclear diatomic molecules, exemplified by the carbon monoxide (CO) molecule, exhibit pronounced minima, which can be related to the shape of their HOMO-electron-density distribution. For the CO molecule we have found an analytical condition for the positions of these minima. We have also shown that the effect of the dressing of the HOMO is twofold: (i) the laser-induced Stark shift decreases the ionization yield and (ii) the laser-induced time-dependent dipole and polarizability change the oscillatory structure of the spectra.

Hasovic, E. [Faculty of Science, University of Sarajevo, Zmaja od Bosne 35, BA-71000 Sarajevo (Bosnia and Herzegowina); Max-Born-Institut, Max-Born-Strasse 2a, DE-12489 Berlin (Germany); Busuladzic, M. [Medical Faculty, University of Sarajevo, Cekalusa 90, BA-71000 Sarajevo (Bosnia and Herzegowina); Becker, W. [Max-Born-Institut, Max-Born-Strasse 2a, DE-12489 Berlin (Germany); Milosevic, D. B. [Faculty of Science, University of Sarajevo, Zmaja od Bosne 35, BA-71000 Sarajevo (Bosnia and Herzegowina); Max-Born-Institut, Max-Born-Strasse 2a, DE-12489 Berlin (Germany); Academy of Sciences and Arts of Bosnia and Herzegovina, Bistrik 7, BA-71000 Sarajevo (Bosnia and Herzegowina)

2011-12-15

204

Disintegration of argon clusters in collisions with highly vibrationally excited SF6 molecules in crossed molecular and cluster beams  

NASA Astrophysics Data System (ADS)

It has been found that collisions of highly vibrationally excited SF6 molecules (with the vibrational energy E vib ? 0.5-2.0 eV) with Ar N clusters (where N ? 30-40 is the number of atoms in a cluster) in crossed molecular and cluster beams result in capture of molecules followed by complete disintegration of the clusters. Possible applications of the effect for selective doping of clusters with molecules, laser separation of isotopes, and selective transport of molecules to the surface are discussed.

Makarov, G. N.; Petin, A. N.

2013-03-01

205

Molecular structure - nonlinear optical property relationships for a series of polymethine and squaraine molecules  

NASA Astrophysics Data System (ADS)

This dissertation reports on the investigation of the relationships between molecular structure and two-photon absorption (2PA) properties for a series of polymethine and squaraine molecules. Current and emerging applications exploiting the quadratic dependence upon laser intensity, such as two-photon fluorescence imaging, three-dimensional microfabrication, optical data storage and optical limiting, have motivated researchers to find novel materials exhibiting strong 2PA. Organic materials are promising candidates because their linear and nonlinear optical properties can be optimized for applications by changing their structures through molecular engineering. Polymethine and squaraine dyes are particularly interesting because they are fluorescent and showing large 2PA. We used three independent nonlinear spectroscopic techniques (Z-scan, two-photon fluorescence and white-light continuum pump-probe spectroscopy) to obtain the 2PA spectra revealing 2PA bands, and we confirm the experimental data by comparing the results from the different methods mentioned. By systematically altering the structure of polyemthines and squaraines, we studied the effects of molecular symmetry, strength of donor terminal groups, conjugation length of the chromophore chain, polarity of solvents, and the effects of placing bridge molecules inside the chromophore chain on the 2PA properties. We also compared polymethine, squaraine, croconium and tetraon dyes with the same terminal groups to study the effects of the different additions inserted within the chromophore chain on their optical properties. Near IR absorbing squaraine dyes were experimentally observed to show extremely large 2PA cross sections (?30000GM). A simplified three-level model was used to fit the measured 2PA spectra and detailed quantum chemical calculations revealed the reasons for the squaraine to exhibit strong 2PA. In addition, two-photon excitation fluorescence anisotropy spectra were measured through multiple 2PA transitions. A theoretical model based on four-levels with two intermediate states was derived and used for analysis of the experimental data.

Fu, Jie

206

Magnesium cation effect on passive diffusion of statin molecules: molecular chromatography approach.  

PubMed

Recently, immobilized artificial membranes (IAMs) have been introduced as HPLC column packing materials. IAMs consist of phosphatidylcholine residues, the most common phospholipids in natural membranes, covalently bound to silica propylamine and consequently mimic fluid phospholipid bilayer. Thus, the immobilized artificial membrane provided a biophysical model system to study the passive diffusion of the statin molecules through the cellular membrane. Statins or 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMG-CoA R) inhibitors are widely used for reducing the circulating atherogenic lipid fractions and decreasing cardiovascular morbidity and mortality. This paper describes magnesium cation (Mg(2+)) effect on five statin molecules (pravastatin, mevastatin, atorvastatin, simvastatin and fluvastatin)-IAM surface association using a molecular chromatography approach. An analysis of the thermodynamics (i.e. enthalpy (DeltaH degrees ), entropy (DeltaS degrees *)) of the interaction of the statin molecules with the immobilized monolayer was also carried out. The DeltaH degrees and DeltaS degrees * values were negative due to van der Waals interactions and hydrogen bonding between the statin molecules with the polar head groups of phospholipid monolayer (polar retention effect). However, the increase of statin-IAM association, with the Mg(2+) concentration increase, was associated with an increase of these thermodynamic data. This explains that this interaction was also governed by hydrophobic and electrostatic bonds which became preponderant. The statin elution order was: Pravastatin

Sarr, Fatimata Seydou; Guillaume, Yves Claude; André, Claire

2008-02-16

207

Ultrafast molecular dynamics of liquid aromatic molecules and the mixtures with CCl4  

NASA Astrophysics Data System (ADS)

The ultrafast molecular dynamics of liquid aromatic molecules, benzene, toluene, ethylbenzene, cumene, and 1,3-diphenylpropane, and the mixtures with CCl4 have been investigated by means of femtosecond optical heterodyne-detected Raman-induced Kerr effect spectroscopy. The picosecond Kerr transients of benzene, toluene, ethylbenzene, and cumene and the mixtures with CCl4 show a biexponential feature. 1,3-Diphenylpropane and the mixtures with CCl4 show triexponential picosecond Kerr transients. The slow relaxation time constants of the aromatic molecules and the mixtures with CCl4 are qualitatively described by the Stoke-Einstein-Debye hydrodynamic model. The ultrafast dynamics have been discussed based on the Kerr spectra in the frequency range of 0-800 cm-1 obtained by the Fourier transform analysis of the Kerr transients. The line shapes of the low-frequency intermolecular spectra located at 0-180 cm-1 frequency range have been analyzed by two Brownian oscillators (~11 cm-1 and ~45 cm-1 peaks) and an antisymmetric Gaussian function (~65 cm-1 peak). The spectrum shape of 1,3-diphenylpropane is quite different from the spectrum shapes of the other aromatic molecules for the low magnitude of the low-frequency mode of 1,3-diphenylpropane and/or an intramolecular vibration. Although the concentration dependences of the low- and intermediate-frequency intermolecular modes (Brownian oscillators) do not show a significant trend, the width of high-frequency intermolecular mode (antisymmetric Gaussian) becomes narrower with the higher CCl4 concentration for all the aromatics mixtures with CCl4. The result indicates that the inhomogeneity of the intermolecular vibrational mode in aromatics/CCl4 mixtures is decreasing with the lower concentration of aromatics. The intramolecular vibrational modes of the aromatic molecules observed in the Kerr spectra are also shown with the calculation results based on the density functional theory.

Shirota, Hideaki

2005-01-01

208

Collision dynamics of methyl radicals and highly vibrationally excited molecules using crossed molecular beams  

SciTech Connect

The vibrational to translational (V{yields}T) energy transfer in collisions between large highly vibrationally excited polyatomics and rare gases was investigated by time-of-flight techniques. Two different methods, UV excitation followed by intemal conversion and infrared multiphoton excitation (IRMPE), were used to form vibrationally excited molecular beams of hexafluorobenzene and sulfur hexafluoride, respectively. The product translational energy was found to be independent of the vibrational excitation. These results indicate that the probability distribution function for V{yields}T energy transfer is peaked at zero. The collisional relaxation of large polyatomic molecules with rare gases most likely occurs through a rotationally mediated process. Photodissociation of nitrobenzene in a molecular beam was studied at 266 nm. Two primary dissociation channels were identified including simple bond rupture to produce nitrogen dioxide and phenyl radical and isomerization to form nitric oxide and phenoxy radical. The time-of-flight spectra indicate that simple bond rupture and isomerization occurs via two different mechanisms. Secondary dissociation of the phenoxy radicals to carbon monoxide and cyclopentadienyl radicals was observed as well as secondary photodissociation of phenyl radical to give H atom and benzyne. A supersonic methyl radical beam source is developed. The beam source configuration and conditions were optimized for CH{sub 3} production from the thermal decomposition of azomethane. Elastic scattering of methyl radical and neon was used to differentiate between the methyl radicals and the residual azomethane in the molecular beam.

Chu, P.M.Y.

1991-10-01

209

Molecular Dynamics Study of the Disruption of H-BONDS by Water Molecules and its Diffusion Behavior in Amorphous Cellulose  

NASA Astrophysics Data System (ADS)

Hydrolysis is an important component of the aging of cellulose, and it severely affects the insulating performance of cellulosic materials. The diffusion behavior of water molecules in amorphous cellulose and their destructive effect on the hydrogen bonding structure of cellulose were investigated by molecular dynamics. The change in the hydrogen bonding structure indicates that water molecules have a considerable effect on the hydrogen bonding structure within cellulose: both intermolecular and intramolecular hydrogen bonds decreased with an increase in ingressive water molecules. Moreover, the stabilities of the cellulose molecules were disrupted when the number of intermolecular hydrogen bonds declined to a certain degree. Both the free volumes of amorphous cells and water molecule-cellulose interaction affect the diffusion of water molecules. The latter, especially the hydrogen bonding interaction between water molecules and cellulose, plays a predominant role in the diffusion behavior of water molecules in the models of which the free volume rarely varies. The diffusion coefficient of water molecules has an excellent correlation with water molecule-cellulose interaction and the average hydrogen bonds between each water molecule and cellulose; however, this relationship was not apparent between the diffusion coefficient and free volume.

Liao, Ruijin; Zhu, Mengzhao; Zhou, Xin; Zhang, Fuzhou; Yan, Jiaming; Zhu, Wenbin; Gu, Chao

2012-06-01

210

Hairpin-bisulfite PCR: Assessing epigenetic methylation patterns on complementary strands of individual DNA molecules  

PubMed Central

Epigenetic inheritance, the transmission of gene expression states from parent to daughter cells, often involves methylation of DNA. In eukaryotes, cytosine methylation is a frequent component of epigenetic mechanisms. Failure to transmit faithfully a methylated or an unmethylated state of cytosine can lead to altered phenotypes in plants and animals. A central unresolved question in epigenetics concerns the mechanisms by which a locus maintains, or changes, its state of cytosine methylation. We developed “hairpin-bisulfite PCR” to analyze these mechanisms. This method reveals the extent of methylation symmetry between the complementary strands of individual DNA molecules. Using hairpin-bisulfite PCR, we determined the fidelity of methylation transmission in the CpG island of the FMR1 gene in human lymphocytes. For the hypermethylated CpG island of this gene, characteristic of inactive-X alleles, we estimate a maintenance methylation efficiency of ?0.96 per site per cell division. For de novo methylation efficiency (Ed), remarkably different estimates were obtained for the hypermethylated CpG island (Ed = 0.17), compared with the hypomethylated island on the active-X chromosome (Ed < 0.01). These results clarify the mechanisms by which the alternative hypomethylated and hypermethylated states of CpG islands are stably maintained through many cell divisions. We also analyzed a region of human L1 transposable elements. These L1 data provide accurate methylation patterns for the complementary strand of each repeat sequence analyzed. Hairpin-bisulfite PCR will be a powerful tool in studying other processes for which genetic or epigenetic information differs on the two complementary strands of DNA.

Laird, Charles D.; Pleasant, Nicole D.; Clark, Aaron D.; Sneeden, Jessica L.; Hassan, K. M. Anwarul; Manley, Nathan C.; Vary, Jay C.; Morgan, Todd; Hansen, R. Scott; Stoger, Reinhard

2004-01-01

211

Extension of a simplified method for molecular correlation energy calculations to molecules containing third row atoms II. Application to HCl, HCl + , ClO and NCl molecules  

Microsoft Academic Search

A simplified method for molecular correlation energy calculations developed in I is applied to the determination of the potential curves of some diatomic chlorinated molecules HCl(1S+), HCl+(2II), ClO(2II) and NCl(X3S-, a1?, b1S+). Dissociation energies, vibrational frequencies and equilibrium internuclear distances are derived from these curves. The ionisation potential (Ip) of HCl, the proton affinity (PA) of Cl, and the term

Jacques Lievin; Jean-Yves Metz

1985-01-01

212

Single quintuple bond [PhCrCrPh] molecule as a possible molecular switch  

NASA Astrophysics Data System (ADS)

The electronic transport properties of a single quintuple bond [PhCrCrPh] molecule sandwiched between two Au(111) surfaces with the trans-bent and linear configurations are studied by a fully self-consistent nonequilibrium Green's function method combined with density functional theory. The calculated transmission spectra of two chemical isomers are remarkablty distinctive. Theoretical results suggest that the current through the trans-bent configuration is significantly larger than the corresponding linear one. The predicted on-off ratio of currents ranging from around 50 to 200 in the applied bias window [-1.5 V, 1.5 V] suggests that multiple bond compounds have attractive potential in molecular switch technology.

Huang, Jing; Li, Qunxiang; Ren, Hao; Su, Haibin; Yang, Jinlong

2006-11-01

213

State-selected ion-molecule reactions with Coulomb-crystallized molecular ions in traps  

NASA Astrophysics Data System (ADS)

State-selected Coulomb-crystallized molecular ions were employed for the first time in ion-molecule reaction studies using the prototypical charge-transfer process N2++N?N+N2+ as an example. By preparing the reactant ions in a well-defined rovibrational state and localizing them in space by sympathetic cooling to milliKelvin temperatures in an ion trap, state- and energy-controlled reaction experiments with sensitivities on the level of single ions were performed. The experimental results were interpreted with quasi-classical trajectory simulations on a six-dimensional potential-energy surface which provided detailed insight into translation-to-rotation energy transfer occurring during charge transfer between N2 and N2+.

Tong, Xin; Nagy, Tibor; Reyes, Juvenal Yosa; Germann, Matthias; Meuwly, Markus; Willitsch, Stefan

2012-09-01

214

Molecular dynamics study of solvation differences between cis- and transplatin molecules in water  

NASA Astrophysics Data System (ADS)

The classical molecular dynamics (MD) simulations for the solvation properties of cis- and transplatins in water are performed with the Lennard-Jones plus Coulomb electrostatic potential parameters that are optimized with ab initio potential energies of the water-platin systems. Two hydration shells are found both for cis- and transplatins. The first shell of water molecules is closer to transplatin than cisplatin. The average number and lifetime of the intermolecular hydrogen bonds (HBs) estimated from the MD trajectories indicate that the Cl and NH3 ligands are the main groups involved in the intermolecular HBs with water. In comparison with cisplatin, there are more HBs around transplatin and these HBs show the longer lifetime. The distinctly different solvation structures between cis- and transplatins are further revealed with the spatially anisotropic distributions of the first hydration shells.

Fu, Cen-Feng; Tian, Shan Xi

2010-05-01

215

Operation mechanism of rotary molecular motor F1 probed by single-molecule techniques  

NASA Astrophysics Data System (ADS)

F1 is a rotary motor protein. Three catalytic ?-subunits in the stator ?3?3 ring are torque generators, and rotate the rotor ?-subunit by sequential and cooperative conformational changes coupled with adenosine triphosphate (ATP) hydrolysis reaction. F1 shows remarkable performances such as rotation rate faster than 10,000 rpm, high reversibility and efficiency in chemo-mechanical energy conversion. I will introduce basic characteristics of F1 revealed by single-molecule imaging and manipulation techniques based on optical microscopy and high-speed atomic force microscopy. I will also discuss the possible operation mechanism behind the F1, along with structurally-related hexameric ATPases, also mentioning the possibility of generating hybrid molecular motors.

Iino, Ryota

2013-03-01

216

The recognition of lysozyme by patterned molecularly imprinted polymers  

Microsoft Academic Search

Microelectro-mechanical-system (MEMS) microsensing devices have recently been extensively researched for their application in biomedical diagnostics. Molecularly imprinted polymers with highly specific binding to targets and their low cost have potential for use in devices as sensing materials. Both techniques were combined to synthesize localized molecularly imprinted polymers (MIPs) by microcontact printing for integration in a micrototal analysis system (?TAS).

Hung-Yin Lin; Dorcas; Cheng-Pu Lin; Gwo-Bin Lee; Tse-Chuan Chou

2005-01-01

217

Characterizing the unfolded states of proteins using single-molecule FRET spectroscopy and molecular simulations  

PubMed Central

To obtain quantitative information on the size and dynamics of unfolded proteins we combined single-molecule lifetime and intensity FRET measurements with molecular simulations. We compared the unfolded states of the 64-residue, ?/? protein L and the 66-residue, all-? cold-shock protein CspTm. The average radius of gyration (Rg) calculated from FRET data on freely diffusing molecules was identical for the two unfolded proteins at guanidinium chloride concentrations >3 M, and the FRET-derived Rg of protein L agreed well with the Rg previously measured by equilibrium small-angle x-ray scattering. As the denaturant concentration was lowered, the mean FRET efficiency of the unfolded subpopulation increased, signaling collapse of the polypeptide chain, with protein L being slightly more compact than CspTm. A decrease in Rg with decreasing denaturant was also observed in all-atom molecular dynamics calculations in explicit water/urea solvent, and Langevin simulations of a simplified representation of the polypeptide suggest that collapse can result from either increased interresidue attraction or decreased excluded volume. In contrast to both the FRET and simulation results, previous time-resolved small-angle x-ray scattering experiments showed no collapse for protein L. Analysis of the donor fluorescence decay of the unfolded subpopulation of both proteins gives information about the end-to-end chain distribution and suggests that chain dynamics is slow compared with the donor life-time of ?2 ns, whereas the bin-size independence of the small excess width above the shot noise for the FRET efficiency distributions may result from incomplete conformational averaging on even the 1-ms time scale.

Merchant, Kusai A.; Best, Robert B.; Louis, John M.; Gopich, Irina V.; Eaton, William A.

2007-01-01

218

A mixed quantum-classical molecular dynamics study of vibrational relaxation of a molecule in solution  

NASA Astrophysics Data System (ADS)

An application of mixed quantum-classical molecular dynamics to vibrational relaxation of the solute molecule in the solution has been investigated. In the present paper, we demonstrate that mean field approximation, rather than surface hopping approximation, works satisfactorily well for the vibrational relaxation of, at least, the CN- ion in the aqueous solution, where the potential surface of the solvent water depends little on the vibrational quantum state of the solute. The calculated relaxation time is in good correspondence to those obtained from other two different methods based upon the same potential model, i.e., Fermi's Golden Rule with classical force autocorrelation function and path integral influence functional theory in its classical bath limit. The present method gives some interesting findings for the relaxation. For example, the energy relaxation time may be longer than the population relaxation time. With respect to the coupling to the solvent, water molecules in the first hydration shell make a leading contribution to the relaxation of the solute.

Terashima, Takeshi; Shiga, Motoyuki; Okazaki, Susumu

2001-04-01

219

High-efficiency molecular counting in solution: Single-molecule detection in electrodynamically focused microdroplet streams  

SciTech Connect

We report fluorescence detection of individual rhodamine 6G molecules using a linear quadrupole to focus streams of microdroplets through the waist of a counterpropagating cw Ar{sup +} laser. Since the terminal velocity scales as the square of the droplet diameter, the droplet-laser interaction time was `tunable` between 5 and 200 ms by using water samples spiked with a small, variable (2-5% v/v) amount of glycerol. Fluorescence bursts from droplets containing single molecules were clearly distinguished from the blanks in real time with an average signal-to-noise ratio of about 10, limited primarily by photobleaching and droplet size fluctuations (<1%). The volume throughput rates associated with this approach (approx. 10 pL/s) are roughly 10{sup 3} higher than those associated with particle levitation techniques, with minimal sacrifice in sensitivity. Total molecular detection efficiencies of about 80% (at >99% confidence) were obtained for 100 and 15 fM rhodamine 6G solutions, in good agreement with detailed theoretical calculations and statistical limitations. 39 refs., 7 figs., 1 tab.

Lermer, N.; Barnes, M.D.; Kung, C.Y.; Whitten, W.B.; Ramsey, J.M. [Oak Ridge National Lab., TN (United States)

1997-06-01

220

Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation  

PubMed Central

The detection and quantification of genetic heterogeneity in populations of cells is fundamentally important to diverse fields, ranging from microbial evolution to human cancer genetics. However, despite the cost and throughput advances associated with massively parallel sequencing, it remains challenging to reliably detect mutations that are present at a low relative abundance in a given DNA sample. Here we describe smMIP, an assay that combines single molecule tagging with multiplex targeted capture to enable practical and highly sensitive detection of low-frequency or subclonal variation. To demonstrate the potential of the method, we simultaneously resequenced 33 clinically informative cancer genes in eight cell line and 45 clinical cancer samples. Single molecule tagging facilitated extremely accurate consensus calling, with an estimated per-base error rate of 8.4 × 10?6 in cell lines and 2.6 × 10?5 in clinical specimens. False-positive mutations in the single molecule consensus base-calls exhibited patterns predominantly consistent with DNA damage, including 8-oxo-guanine and spontaneous deamination of cytosine. Based on mixing experiments with cell line samples, sensitivity for mutations above 1% frequency was 83% with no false positives. At clinically informative sites, we identified seven low-frequency point mutations (0.2%–4.7%), including BRAF p.V600E (melanoma, 0.2% alternate allele frequency), KRAS p.G12V (lung, 0.6%), JAK2 p.V617F (melanoma, colon, two lung, 0.3%–1.4%), and NRAS p.Q61R (colon, 4.7%). We anticipate that smMIP will be broadly adoptable as a practical and effective method for accurately detecting low-frequency mutations in both research and clinical settings.

Hiatt, Joseph B.; Pritchard, Colin C.; Salipante, Stephen J.; O'Roak, Brian J.; Shendure, Jay

2013-01-01

221

The serum mannose-binding protein and the macrophage mannose receptor are pattern recognition molecules that link innate and adaptive immunity  

Microsoft Academic Search

The innate immune system evolved to protect the host in the early phases of an infectious challenge. The soluble mannose binding protein, and the cell surface mannose receptor are two key pattern recognition molecules of innate immunity. The ligand binding specificity of these molecules enables them to differentiate ‘self’ from ‘non-self’. These pattern recognition capabilities are coupled to effector functions,

Iain P Fraser; Henry Koziel; R. Alan B Ezekowitz

1998-01-01

222

Small-molecule inhibitors of cathepsin L incorporating functionalized ring-fused molecular frameworks.  

PubMed

Cathepsin L is a cysteine protease that is upregulated in a variety of malignant tumors and plays a significant role in cancer cell invasion and migration. It is an attractive target for the development of small-molecule inhibitors, which may prove beneficial as treatment agents to limit or arrest cancer metastasis. We have previously identified a structurally diverse series of thiosemicarbazone-based inhibitors that incorporate the benzophenone and thiochromanone molecular scaffolds. Herein we report an important extension of this work designed to explore fused aryl-alkyl ring molecular systems that feature nitrogen atom incorporation (dihydroquinoline-based) and carbon atom exclusivity (tetrahydronaphthalene-based). In addition, analogues that contain oxygen (chromanone-based), sulfur (thiochroman-based), sulfoxide, and sulfone functionalization have been prepared in order to further investigate the structure-activity relationship aspects associated with these compounds and their ability to inhibit cathepsins L and B. From this small-library of 30 compounds, five were found to be strongly inhibitory (IC50 <500 nM) against cathepsin L with the most active compound (7-bromodihydroquinoline thiosemicarbazone 48) demonstrating an IC50=164 nM. All of the compounds evaluated were inactive (IC50 >10,000 nM) as inhibitors of cathepsin B, thus establishing a high degree (>20-fold) of selectivity (cathepsin L vs. cathepsin B) for the most active cathepsin L inhibitors in this series. PMID:23540644

Song, Jiangli; Jones, Lindsay M; Chavarria, Gustavo E; Charlton-Sevcik, Amanda K; Jantz, Adam; Johansen, Audra; Bayeh, Liela; Soeung, Victoria; Snyder, Lindsey K; Lade, Shawn D; Chaplin, David J; Trawick, Mary Lynn; Pinney, Kevin G

2012-12-20

223

Stochastic molecular dynamics study of trans-gauche isomerization processes in simple chain molecules  

NASA Astrophysics Data System (ADS)

Trans-gauche isomerization rates for n-butane, n-pentane, and n-decane are determined from a stochastic molecular dynamics calculation of the reactive fluxes. Analysis of the deviations of these rates from the transition state theory predictions shows that the transmission coefficients differ markedly from unity for all physically realizable conditions. The dependence of the transmission coefficient on the collision frequency or friction constant parameterizing the stochastic element is discussed. A comparison between the stochastic dynamics and a true Newtonian molecular dynamics simulation of n-butane in a simple liquid solvent indicates that the reactive flux correlation function is significantly different than would be predicted by the high friction noninertial theory first discussed long ago by Kramers. For longer chain molecules, the isomerization rates depend upon which particular torsional angle is considered, and upon the configurational state of the neighboring angles. This dependence is analyzed. Finally, calculations are presented which address certain questions concerning the use of holonomic constraints in the dynamics of alkane chains.

Montgomery, John A.; Holmgren, Stephen L.; Chandler, David

1980-10-01

224

Molecular Quantum Spintronics: Supramolecular Spin Valves Based on Single-Molecule Magnets and Carbon Nanotubes  

PubMed Central

We built new hybrid devices consisting of chemical vapor deposition (CVD) grown carbon nanotube (CNT) transistors, decorated with TbPc2 (Pc = phthalocyanine) rare-earth based single-molecule magnets (SMMs). The drafting was achieved by tailoring supramolecular ?-? interactions between CNTs and SMMs. The magnetoresistance hysteresis loop measurements revealed steep steps, which we can relate to the magnetization reversal of individual SMMs. Indeed, we established that the electronic transport properties of these devices depend strongly on the relative magnetization orientations of the grafted SMMs. The SMMs are playing the role of localized spin polarizer and analyzer on the CNT electronic conducting channel. As a result, we measured magneto-resistance ratios up to several hundred percent. We used this spin valve effect to confirm the strong uniaxial anisotropy and the superparamagnetic blocking temperature (TB ~ 1 K) of isolated TbPc2 SMMs. For the first time, the strength of exchange interaction between the different SMMs of the molecular spin valve geometry could be determined. Our results introduce a new design for operable molecular spintronic devices using the quantum effects of individual SMMs.

Urdampilleta, Matias; Nguyen, Ngoc-Viet; Cleuziou, Jean-Pierre; Klyatskaya, Svetlana; Ruben, Mario; Wernsdorfer, Wolfgang

2011-01-01

225

Pattern Speeds of BIMA SONG Galaxies with Molecule-dominated Interstellar Mediums Using the Tremaine-Weinberg Method  

NASA Astrophysics Data System (ADS)

We apply the Tremaine-Weinberg method of pattern speed determination to data cubes of CO emission in six spiral galaxies from the BIMA Survey of Nearby Galaxies, each with an interstellar medium dominated by molecular gas. We compare derived pattern speeds with estimates based on other methods, usually involving the identification of a predicted behavior at one or more resonances of the pattern(s). In two cases (NGC 1068 and NGC 4736), we find evidence for a central bar pattern speed that is greater than that of the surrounding spiral and roughly consistent with previous estimates. However, the spiral pattern speed in both cases is much larger than previous determinations. For the barred spirals NGC 3627 and NGC 4321, the method is insensitive to the bar pattern speed (the bar in each is nearly parallel to the major axis; in this case the method will not work), but for the former galaxy the spiral pattern speed found agrees with previous estimates of the bar pattern speed, suggesting that these two structures are part of a single pattern. For the latter, the spiral pattern speed found is in agreement with several previous determinations. For the flocculent spiral NGC 4414 and the ``Evil Eye'' galaxy NGC 4826, the method does not support the presence of a large-scale coherent pattern. We also apply the method to a simulated barred galaxy in order to demonstrate its validity and to understand its sensitivity to various observational parameters. In addition, we study the results of applying the method to a simulated, clumpy axisymmetric disk with no wave present. The Tremaine & Weinberg method in this case may falsely indicate a well-defined pattern.

Rand, Richard J.; Wallin, John F.

2004-10-01

226

Evaluation of Spartan semi-empirical molecular modeling software for calculations of molecules on surfaces: CO adsorption on Ni(111).  

PubMed

This paper reports the use of the PM3(tm) semi-empirical method in the Spartan molecular modeling software to optimize geometries and calculate vibrational frequencies for increasingly complex transition metal- and carbon monoxide (CO)-containing systems, culminating in calculations of CO adsorbed on a Ni(111) surface. Mononuclear and dinuclear transition metal carbonyl molecular species were used to establish the level of accuracy that could be expected for vibrational frequencies to provide a context for the results from the adsorbed molecule calculations. One to four CO molecules adsorbed on the (111) face of a 22-atom-nickel crystal were then modeled, and the accuracy of the adsorption geometry and vibrational frequency was evaluated. The calculated CO stretching vibrational frequencies were within 8% larger than the gas phase experimental values for the molecular species and were approximately 10% larger than the range of experimental values for CO on the nickel surface. The geometry optimization predicted that the CO molecules on the Ni(111) surface occupy three-fold hollow sites with no preference for sites over Ni atoms, in agreement with recent structural data and other theoretical calculations. The software was less successful in calculating the CO bond angle to the surface and the distance of the CO molecules from the surface, but the calculation did produce a reasonable distance between CO molecules on the surface. In general, the PM3(tm) method in Spartan shows promise for predicting adsorption sites and vibrational frequencies of molecules on metal surfaces. PMID:11219429

Zakharian, T Y; Coon, S R

2001-03-01

227

Researchers use changes in the patterns of sugar molecules to detect cells before they develop into esophageal cancer:  

Cancer.gov

Scientists working at Britain's Medical Research Council, in collaboration with researchers from New York University, have identified changes in the patterns of sugar molecules that line pre-cancerous cells in the esophagus, a condition called Barrett’s dysplasia, making it much easier to detect and remove these cells before they develop into esophageal cancer. These findings, reported in the journal Nature Medicine, have important implications for patients and may help to monitor their condition and prevent the development of cancer.

228

Efficient small molecule bulk heterojunction solar cells with high fill factors via pyrene-directed molecular self-assembly.  

PubMed

Efficient organic photovoltaic (OPV) materials are constructed by attaching completely planar, symmetric end-groups to donor-acceptor electroactive small molecules. Appending C2-pyrene as the small molecule end-group to a diketopyrrolopyrrole core leads to materials with a tight, aligned crystal packing and favorable morphology dictated by ?-? interactions, resulting in high power conversion efficiencies and high fill factors. The use of end-groups to direct molecular self-assembly is an effective strategy for designing high-performance small molecule OPV devices. PMID:22021084

Lee, Olivia P; Yiu, Alan T; Beaujuge, Pierre M; Woo, Claire H; Holcombe, Thomas W; Millstone, Jill E; Douglas, Jessica D; Chen, Mark S; Fréchet, Jean M J

2011-10-21

229

PDMS-Glass bonding using grafted polymeric adhesive - Alternative process flow for compatibility with patterned biological molecules  

PubMed Central

We report a novel modification of silicone elastomer, polydimethylsiloxane (PDMS) with a polymer graft that allows interfacial bonding between elastomer and glass substrate to be performed without exposure of said substrate to harsh treatment conditions like oxygen plasma. Organic molecules can thus be patterned within microfluidic channels and still remain functional post-bonding. In addition, after polymer grafting the PDMS can be stored in a desiccator for at least 40 days, and activated upon exposure to acidic buffer for bonding. The bonded devices remain fully bonded in excess of 80 psi driving pressure, with no signs of compromise to the bond integrity. Finally, we demonstrate the compatibility of our method with biological molecules using a proof-of-concept DNA sensing device, in which fluorescently-labelled DNA targets are successfully captured by a patterned probe in a device sealed using our method, while the pattern on a plasma-treated device was completely destroyed. Therefore, this method provides a much-needed alternative bonding process for incorporation of biological molecules in microfluidic devices.

Beh, Cyrus Weijie; Zhou, Weizhuang

2013-01-01

230

High-Resolution Electron Beam Lithography and DNA Nano-Patterning for Molecular QCA  

Microsoft Academic Search

Electron beam lithography (EBL) patterning of poly(methylmethacrylate) (PMMA) is a versatile tool for defining molecular structures on the sub-10-nm scale. We demonstrate lithographic resolution to about 5 nm using a cold-development technique. Liftoff of sub-10-nm Au nanoparticles and metal lines proves that cold development completely clears the PMMA residue on the exposed areas. Molecular liftoff is performed to pattern DNA

Koshala Sarveswaran; Marya Lieberman; Gary Bernstein

2005-01-01

231

[Participation of damage-associated molecular patterns in conventional treatment of cancer].  

PubMed

Cells of the innate immune system are involved in discriminating between the innocuous cell death (apoptosis) which occurs in tissues during homeostasis, and the cell death associated to tissue damage (necrosis). Recently, a new variant of apoptosis termed immunogenic apoptosis has been described. In cancer, this type of cell death has acquired great relevance. In vitro and in vivo experimental models support that radiotherapy and some chemotherapeutic drugs induce the immunogenic apoptosis of malignant cells. Dying cells express at cytoplasmic membrane or release several nuclear or intracytoplasmic molecules termed "danger signals" or damage associated molecular patterns (DAMPs). DAMPs alert the organism and play a role inducing an efficient anti-tumor immune response. In this review, the importance of cell death by immunogenic apoptosis, the cytotoxic drugs that induce this type of cell death, the biologic role of some DAMPs and their participation in the activation of the antitumor immune response, in particular in the phagocytic cell, are indicated. The goal of this information should impact in improving the participation of the immune system in the recognition and efficient elimination of the residual tumor cells and to overcome the evasion mechanisms of tumor cells. This knowledge should lead to a better control of the growth of tumors with a concomitant reduction in the tumor recurrence. Also, an increase in the survival of the cancer patients or probably their definitive cure could be reached in the future. PMID:23045951

Rojo-León, Verónica; Aguilar-Cázares, Dolores; Prado-García, Heriberto; Carlos-Reyes, Angeles; López-González, José Sullivan

232

Development of the relaxation-assisted 2DIR method for accessing structures of molecules and its application for studying the energy transport on a molecular level  

NASA Astrophysics Data System (ADS)

Measuring the three-dimensional structure of molecules, dynamics of structural changes, and energy transport on a molecular scale is important for many areas of natural science. Supplementing the widely used methods of x-ray diffraction, NMR, and optical spectroscopies, a two-dimensional infrared spectroscopy (2DIR) method was introduced about a decade ago. The 2DIR method measures pair-wise interactions between vibrational modes in molecules, thus acquiring molecular structural constraints such as distances between vibrating groups and the angles between their transition dipoles. The 2DIR method has been applied to a variety of molecular systems but in studying larger molecules such as proteins and peptides the method is facing challenges associated with the congestion of their vibrational spectra and delocalized character of their vibrational modes. To help extract structural information from such spectra and make efficient use of vibrational modes separated by large distances, a novel relaxation-assisted 2DIR method (RA 2DIR) has recently been proposed, which exploits the transport of excess vibrational energy from the initially excited mode. With the goal of further development of RA 2DIR, we applied it to a variety of molecular systems, including model compounds, transition-metal complexes, and isomers. The experiments revealed several novel effects which both enhance the power of RA 2DIR and bring a deeper understanding to the fundamental process of energy transport on a molecular level. We demonstrated that RA 2DIR can enhance greatly (27-fold) the cross-peak amplitude among spatially remote modes, which leads to an increase of the range of distances accessible for structural measurements by several fold. We demonstrated that the energy transport time correlates with the intermode distance. This correlation offers a new way for identifying connectivity patterns in molecules. We developed two models of energy transport in molecules. In one, a spatial overlap of vibrational modes determines the rate of energy transfer. Another model uses generalizations of Marcus theory of electron transfer applied to anharmonic vibrational transitions. These theoretical models reproduce well the main features of RA 2DIR measurements in a set of isomers where the energy transport is found to be affected by the three-dimensional structure as well as in transition-metal complexes, where the energy transport has to go through relatively weak coordination bonds and can be different from that occurring via covalent bonds.

Kasyanenko, Valeriy Mitrofanovich

233

Molecular dynamics study of structure H clathrate hydrates of methane and large guest molecules  

NASA Astrophysics Data System (ADS)

Methane storage in structure H (sH) clathrate hydrates is attractive due to the relatively higher stability of sH as compared to structure I methane hydrate. The additional stability is gained without losing a significant amount of gas storage density as happens in the case of structure II (sII) methane clathrate. Our previous work has showed that the selection of a specific large molecule guest substance (LMGS) as the sH hydrate former is critical in obtaining the optimum conditions for crystallization kinetics, hydrate stability, and methane content. In this work, molecular dynamics simulations are employed to provide further insight regarding the dependence of methane occupancy on the type of the LMGS and pressure. Moreover, the preference of methane molecules to occupy the small (512) or medium (435663) cages and the minimum cage occupancy required to maintain sH clathrate mechanical stability are examined. We found that thermodynamically, methane occupancy depends on pressure but not on the nature of the LMGS. The experimentally observed differences in methane occupancy for different LMGS may be attributed to the differences in crystallization kinetics and/or the nonequilibrium conditions during the formation. It is also predicted that full methane occupancies in both small and medium clathrate cages are preferred at higher pressures but these cages are not fully occupied at lower pressures. It was found that both small and medium cages are equally favored for occupancy by methane guests and at the same methane content, the system suffers a free energy penalty if only one type of cage is occupied. The simulations confirm the instability of the hydrate when the small and medium cages are empty. Hydrate decomposition was observed when less than 40% of the small and medium cages are occupied.

Susilo, Robin; Alavi, Saman; Ripmeester, John A.; Englezos, Peter

2008-05-01

234

Molecular patterning mechanism underlying metamorphosis of the thoracic leg in Manduca sexta  

Microsoft Academic Search

The tobacco hornworm Manduca sexta, like many holometabolous insects, makes two versions of its thoracic legs. The simple legs of the larva are formed during embryogenesis, but then are transformed into the more complex adult legs at metamorphosis. To elucidate the molecular patterning mechanism underlying this biphasic development, we examined the expression patterns of five genes known to be involved

Kohtaro Tanaka; James W. Truman

2007-01-01

235

Molecular dynamics simulations on the aggregation behavior of indole type organic dye molecules in dye-sensitized solar cells.  

PubMed

In Ti0(2) nanostructured dye-sensitized solar cells indole based organic dyes D149, D205 exhibits greater power conversion efficiency. Such organic dye molecules are easily undergone for aggregation. Aggregation in dye molecules leads to reduce electron transfer process in dye-sensitized solar cells. Therefore, anti-aggregating agents such as chenodeoxycholic acid are commonly added to organic dye solution in DSSCs. Studying aggregation of such dye molecules in the absence of semiconductors gives a detailed influence of anti-aggregating agents on dye molecules. Atomistic level of molecular dynamics (MD) simulations were performed on aggregation of indole type dye molecules D149, D205 and D205-F with anti-aggregating agent chenodeoxy cholic acid using AMBER program. The trajectories of the MD simulations were analyzed with order parameters such as radial atom pair distribution functions g(r), diffusion coefficients and root mean square deviations values. MD results suggest that addition of chenodeoxy cholic acid to dyes significantly reduces structural arrangement and increases conformational flexibility and mobility of dye molecules. The influence of semi-perfluorinated alkyl chains in indole dye molecules was analyzed. The parameters such as open-circuit voltage (V(oc)) and power conversion efficiency (?) of dye-sensitized solar cells are corroborated with flexibility and diffusion values of dye molecules. PMID:21904812

Selvaraj, Ananda Rama Krishnan; Hayase, Shuji

2011-09-09

236

Low molecular weight molecules of oyster nacre induce mineralization of the MC3T3-E1 cells.  

PubMed

The nacre layer from the pearl oyster shell is considered as a promising osteoinductive biomaterial. Nacre contains one or more signal molecules capable of stimulating bone formation. The identity and the mode of action of these molecules on the osteoblast differentiation were analyzed. Water-soluble molecules from nacre were fractionated according to dialysis, solvent extraction, and reversed-phase HPLC. The activity of a fraction composed of low molecular weight molecules in the mineralization of the MC3T3-E1 extracellular matrix was investigated. Mineralization of the preosteoblast cells was monitored according to alizarin red staining, Raman spectroscopy, scanning electron microscopy, and quantitative RT-PCR. Molecules isolated from nacre, ranging from 50 to 235 Da, induced a red alizarin staining of the preosteoblasts extracellular matrix after 16 days of culture. Raman spectroscopy demonstrated the presence of hydroxyapatite (HA) in samples treated with these molecules. Scanning electron microscopy pictures showed at the surface of the treated cells the occurrence of clusters of spherical particles resembling to HA. The treatment of cells with nacre molecules accelerated expression of collagen I and increased the mRNA expression of Runx2 and osteopontin. This study indicated that the nacre molecules efficient in bone cell differentiation are certainly different from proteins, and could be useful for in vivo bone repair. PMID:17729263

Rousseau, Marthe; Boulzaguet, Hélène; Biagianti, Julie; Duplat, Denis; Milet, Christian; Lopez, Evelyne; Bédouet, Laurent

2008-05-01

237

Patterning of polypyrrole using a fluoropolymer as an adsorption-protecting molecule  

Microsoft Academic Search

Patterning of the conducting polymer polypyrrole (PPy) was achieved using perfluoropolyether (PFPE) as a mask material. The fluoropolymer PFPE has both hydrophobic and oleophobic properties that allowed the generation of passivated patterns against PPy deposition. We exploited these properties to achieve the selective micropattern deposition of PPy, by simple chemical oxidation in an aqueous solution. Using a microcontact printing method,

Sunil Kwon; Jong-Wook Ha; Jiwhan Noh; Sang-Yup Lee

2010-01-01

238

Susceptibility Patterns and Molecular Identification of Trichosporon Species  

Microsoft Academic Search

The physiological patterns, the sequence polymorphisms of the internal transcriber spacer (ITS), and intergenic spacer regions (IGS) of the rRNA genes and the antifungal susceptibility profile were evaluated for their ability to identify Trichosporon spp. and their specificity for the identification of 49 clinical isolates of Trichosporon spp. Morphological and biochemical methodologies were unable to differentiate among the Trichosporon species.

Juan L. Rodriguez-Tudela; Teresa M. Diaz-Guerra; Emilia Mellado; Virginia Cano; Cecilia Tapia; Alexander Perkins; Alicia Gomez-Lopez; Laura Rodero; Manuel Cuenca-Estrella

2005-01-01

239

Cold and heat pattern of rheumatoid arthritis in traditional Chinese medicine: distinct molecular signatures indentified by microarray expression profiles in CD4-positive T cell.  

PubMed

The research is aimed to explore the distinct molecular signatures in discriminating the rheumatoid arthritis patients with traditional Chinese medicine (TCM) cold pattern and heat pattern. Twenty patients with typical TCM cold pattern and heat pattern were included. Microarray technology was used to reveal gene expression profiles in CD4+ T cells. The signal intensity of each expressed gene was globally normalized using the R statistics program. The ratio of cold pattern to heat pattern in patients with RA at more or less than 1:2 was taken as the differential gene expression criteria. Protein-protein interaction information for these genes from databases was searched, and the highly connected regions were detected by IPCA algorithm. The significant pathways were extracted from these subnetworks by Biological Network Gene Ontology tool. Twenty-nine genes differentially regulated between cold pattern and heat pattern were found. Among them, 7 genes were expressed significantly more in cold pattern. Biological network of protein-protein interaction information for these significant genes were searched and four highly connected regions were detected by IPCA algorithm to infer significant complexes or pathways in the biological network. Particularly, the cold pattern was related to Toll-like receptor signaling pathway. The following related pathways in heat pattern were included: Calcium signaling pathway; cell adhesion molecules; PPAR signaling pathway; fatty acid metabolism. These results suggest that better knowledge of the main biological processes involved at a given pattern in TCM might help to choose the most appropriate treatment. PMID:20658292

Lu, Cheng; Xiao, Cheng; Chen, Gao; Jiang, Miao; Zha, Qinglin; Yan, Xiaoping; Kong, Weiping; Lu, Aiping

2010-07-25

240

Synthesis and Magnetism of High Curie Temperature Prussian Blue Analogue Molecular Nanomagnet-Chromium Cyanide Molecule Nanowire Arrays  

Microsoft Academic Search

The goal to synthesize molecular nanomagnets that exhibit spontaneous magnetic ordering close to room temperature might enable one to apply them in the fields of magnetic memory devices and microelectronics. Chromium cyanide molecule nanowire arrays with diameters of about 50 nm and lengths up to 4mum have been synthesized by an electrodepositing technology based on anodizing anodic aluminum oxide films.

Pingheng Zhou; Desheng Xue; Jinli Yao

2009-01-01

241

Determination of NMR lineshape anisotropy of guest molecules within inclusion complexes from molecular dynamics simulations.  

PubMed

Nonspherical cages in inclusion compounds can result in non-uniform motion of guest species in these cages and anisotropic lineshapes in NMR spectra of the guest. Herein, we develop a methodology to calculate lineshape anisotropy of guest species in cages based on molecular dynamics simulations of the inclusion compound. The methodology is valid for guest atoms with spin 1/2 nuclei and does not depend on the temperature and type of inclusion compound or guest species studied. As an example, the nonspherical shape of the structure I (sI) clathrate hydrate large cages leads to preferential alignment of linear CO(2) molecules in directions parallel to the two hexagonal faces of the cages. The angular distribution of the CO(2) guests in terms of a polar angle theta and azimuth angle phi and small amplitude vibrational motions in the large cage are characterized by molecular dynamics simulations at different temperatures in the stability range of the CO(2) sI clathrate. The experimental (13)C NMR lineshapes of CO(2) guests in the large cages show a reversal of the skew between the low temperature (77 K) and the high temperature (238 K) limits of the stability of the clathrate. We determine the angular distributions of the guests in the cages by classical MD simulations of the sI clathrate and calculate the (13)C NMR lineshapes over a range of temperatures. Good agreement between experimental lineshapes and calculated lineshapes is obtained. No assumptions regarding the nature of the guest motions in the cages are required. PMID:18386265

Alavi, Saman; Dornan, Peter; Woo, Tom K

2008-04-21

242

Direct Molecular Simulation of Gradient-Driven Diffusion of Large Molecules using Constant Pressure  

SciTech Connect

Dual control volume grand canonical molecular dynamics (DCV-GCMD) is a boundary-driven non-equilibrium molecular dynamics technique for simulating gradient driven diffusion in multi-component systems. Two control volumes are established at opposite ends of the simulation box. Constant temperature and chemical potential of diffusing species are imposed in the control volumes. This results in stable chemical potential gradients and steady-state diffusion fluxes in the region between the control volumes. We present results and detailed analysis for a new constant-pressure variant of the DCV-GCMD method in which one of the diffusing species for which a steady-state diffusion flux exists does not have to be inserted or deIeted. Constant temperature, pressure and chemical potential of all diffusing species except one are imposed in the control volumes. The constant-pressure method can be applied to situations in which insertion and deletion of large molecules would be prohibitively difficult. As an exampIe, we used the method to shnulate diffusion in a biruuy mixture of spherical particles with a 2:1 size ratio. Steady-state diffusion fluxes of both diffbsi.ng species were established. The constant-pressure diffision coefficients agreed closely with the results of the standard constant-volume calculations. In addition, we show how the concentration, chemical potential and flux profiles can be used to calculate kwd binary and Maxwell-Stefim diffusion coefficients. In the case of the 2:1 size ratio mixture, we found that the binary dlffision coefficients were asymmetric and composition dependent, whereas the Maxwell-Stefan diffision coefficients changed very little with composition and were symmetric. This last result verified that the Gibbs-Duhem relation was satisfied locally, thus validating the assumption of local equilibrium.

Heffelfinger, G.S.; Thompson, A.P.

1998-12-23

243

Lipoteichoic acid is an important microbe-associated molecular pattern of Lactobacillus rhamnosus GG  

PubMed Central

Background Probiotic bacteria are increasingly used as immunomodulatory agents. Yet detailed molecular knowledge on the immunomodulatory molecules of these bacteria is lagging behind. Lipoteichoic acid (LTA) is considered a major microbe-associated molecular pattern (MAMP) of Gram-positive bacteria. However, many details and quantitative data on its immune signalling capacity are still unknown, especially in beneficial bacteria. Recently, we have demonstrated that a dltD mutant of the model probiotic Lactobacillus rhamnosus GG (LGG), having modified LTA molecules, has an enhanced probiotic efficacy in a DSS-induced colitis model as compared to wild-type. Results In this study, the importance of D-alanylated and acylated LTA for the pro-inflammatory activity of LGG was studied in vitro. Purified native LTA of LGG wild-type exhibited a concentration-dependent activation of NF-?B signalling in HEK293T cells after interaction with TLR2/6, but not with TLR2 alone. Chemical deacylation of LTA interfered with the TLR2/6 interaction, while a moderate effect was observed with chemical dealanylation. Similarly, the dltD mutant of LGG exhibited a significantly reduced capacity to activate TLR2/6-dependent NF-?B signalling in a HEK293T reporter cell line compared to wild-type. In addition, the dltD mutant of LGG showed a reduced induction of mRNA of the chemokine IL-8 in the Caco-2 epithelial cell line compared to wild-type. Experiments with highly purified LTA of LGG confirmed that LTA is a crucial factor for IL-8 mRNA induction in Caco-2 epithelial cells. Chemical dealanylation and deacylation reduced IL-8 mRNA expression. Conclusions Taken together, our results indicate that LTA of LGG is a crucial MAMP with pro-inflammatory activities such as IL-8 induction in intestinal epithelial cells and NF-?B induction in HEK293T cells via TLR2/6 interaction. The lipid chains of LGG LTA are needed for these activities, while also the D-alanine substituents are important, especially for IL-8 induction in Caco-2 cells.

2012-01-01

244

Angle-Resolved High-Order Above-Threshold Ionization of a Molecule: Sensitive Tool for Molecular Characterization  

SciTech Connect

The strong-field approximation for ionization of diatomic molecules by an intense laser field is generalized to include rescattering of the ionized electron off the various centers of its molecular parent ion. The resulting spectrum and its interference structure strongly depend on the symmetry of the ground state molecular orbital. For N{sub 2}, if the laser polarization is perpendicular to the molecular axis, we observe a distinct minimum in the emission spectrum, which survives focal averaging and allows determination of, e.g., the internuclear separation. In contrast, for O{sub 2}, rescattering is absent in the same situation.

Busuladzic, M. [Medical Faculty, University of Sarajevo, Cekalusa 90, 71000 Sarajevo (Bosnia and Herzegowina); Gazibegovic-Busuladzic, A. [Faculty of Science, University of Sarajevo, Zmaja od Bosne 35, 71000 Sarajevo (Bosnia and Herzegowina); Milosevic, D. B. [Faculty of Science, University of Sarajevo, Zmaja od Bosne 35, 71000 Sarajevo (Bosnia and Herzegowina); Max-Born-Institut, Max-Born-Strasse 2a, 12489 Berlin (Germany); Becker, W. [Max-Born-Institut, Max-Born-Strasse 2a, 12489 Berlin (Germany)

2008-05-23

245

Resonance enhanced multiphoton ionization spectra of molecules and molecular fragments. Annual technical report  

SciTech Connect

Resonance Enhanced Multiphoton Ionization (REMPI) utilizes pulsed laser radiation to prepare a molecule in an excited state via absorption of one or more photons and to subsequently ionize that state before it can decay. A remarkable feature of REMPI, and one that is very basic to many of its applications and uses, is that the very narrow bandwidth of the {open_quotes}pump{close_quotes} laser makes it possible to select a specific vibrational and rotational level in the initial state and to prepare the excited state of interest in a single vibrational and rotational level. Thus, by suitable choice of the photon pump transition, it is possible to selectively ionize a species of interest without ionizing any other species that might be present. This feature makes REMPI one of the most powerful tools for ultrasensitive detection of species. With REMPI it is also possible to study the photoionization dynamics of a single rotational level of an excited electronic state. Such state-resolved studies can certainly be expected to provide significant insight into the underlying dynamics of molecular photoionization.

NONE

1997-07-01

246

Structures of molecules in ground and excited vibrational states from quasiclassical direct ab initio molecular dynamics.  

PubMed

We demonstrate that the mean structures of molecules derived from quasiclassical direct ab initio molecular dynamics (MD) simulation, the classical simulation that takes into account quantum vibrational levels, agree well with those determined from quantum-mechanical (QM) expectation values and/or experimentally observed values. First, for a one-dimensional model potential that includes anharmonicity as the third-order potential energy term, we show that the time-averaged structure over the classical trajectory with taking account of a quantum vibrational energy level correlates with a QM structure averaged using a vibrational wave function based on the first-order perturbation theory. Next, quasiclassical direct ab initio MD and Fourier grid Hamiltonian method are applied to OH and OD radicals; the mean structures at several vibrational levels of both classical and QM methods coincide, and they are in good agreement with the structures determined experimentally. Quasiclassical direct ab initio MD is then applied to H(2)O, C(2)H(2), and C(6)H(6). For H(2)O and C(2)H(2), the classical mechanically calculated mean structural parameters agree well with the experimental values and the QM values obtained from vibrational self-consistent field. For C(2)H(2), we find that r(g)(C-H) is longer than r(e)(C-H), whereas r(mean)((0))(C-H), which is equal to r(z)(C-H), is slightly shorter than r(e)(C-H). PMID:20455585

Yamada, Tomonori; Aida, Misako

2010-06-01

247

Species Classification and Rotational Energy Level Patterns of Non-Linear Triatomic Molecules  

Microsoft Academic Search

With the object of making existing knowledge more readily available, the quantized energy levels of symmetrical and asymmetrical tops are discussed from the viewpoint of their classification into species defined by symmetry operations; and simple species nomenclatures are proposed. These are then applied in a discussion of the rotational levels of symmetrical non-linear triatomic molecules AB2. With SO2 as an

Robert S. Mulliken

1941-01-01

248

Molecular architecture of zinc chelating small molecules that inhibit spliceosome assembly at an early stage  

PubMed Central

The removal of intervening sequences (introns) from a primary RNA transcript is catalyzed by the spliceosome, a large ribonucleoprotein complex. At the start of each splicing cycle, the spliceosome assembles anew in a sequentially ordered manner on the pre-mRNA intron to be removed. We describe here the identification of a series of naphthalen-2-yl hydroxamate compounds that inhibit pre-mRNA splicing in vitro with mid- to high-micromolar values of IC50. These hydroxamates stall spliceosome assembly at the A complex stage. A structure–activity analysis of lead compounds revealed three pharmacophores that are essential for splicing inhibition. Specifically, a hydroxamate as a zinc-binding group and a 6-methoxynaphthalene cap group are both critical, and a linker chain comprising eight to nine methylene groups is also important, for the specific binding to the docking site of a target protein molecule and precise positioning of the zinc binding group. As we found no correlation between the inhibition patterns of known histone deacetylases on the one hand and pre-mRNA splicing on the other, we conclude that these compounds may function through the inhibition of the activities of other, at present, unknown spliceosome-associated zinc metalloprotein(s).

Patil, Vishal; Canzoneri, Josh C.; Samatov, Timur R.; Luhrmann, Reinhard; Oyelere, Adegboyega K.

2012-01-01

249

Ion and molecule sensors using molecular recognition in luminescent, conductive polymers. FY 1997 year-end progress report  

SciTech Connect

'The purpose of this project is to use molecular recognition strategies to develop sensor technology based on luminescent, conductive polymers that contain sites for binding specific molecules or ions in the presence of related molecules or ions. Selective binding of a particular molecule or ion of interest to these polymers will result in a large change in their luminescence and/or conductivity, which can be used to both qualitatively and quantitatively sense the presence of the bound molecules or ions. The main thrusts and accomplishments in the first year of this project involve developing polymer syntheses that yield conjugated polymers to which a wide variety of ligands for metal ion binding can be readily incorporated.'

Wasielewski, M.R.

1997-01-01

250

Luminescences of Pyrene Single Crystal and Pyrene Molecules Inserted in a Molecular Vessel of Cyclodextrin  

Microsoft Academic Search

Highly purified single crystals of pyrene were made by a gas phase crystal growth method from 180 times of zone-refined pyrene. The dry powder of beta-cyclodextrin including a pyrene single molecule and that of gamma-cyclodextrin including twin molecules were prepared under vacuum. The luminescence spectra of pyrene single molecules, twin molecules and single crystals, and their temperature dependences were measured

Nobuaki Takahashi; Bold Gombojav; Takehisa Yoshinari; Yoshio Takahashi; Shin-ichiro Nagasaka; Aishi Yamamoto; Takenari Goto; Atsuo Kasuya

2007-01-01

251

Earle K. Plyler Prize for Molecular Spectroscopy Talk: Coherent Ultrafast Multidimensional Spectroscopy of Molecules; From NMR to X-rays  

NASA Astrophysics Data System (ADS)

Multidimensional spectroscopic techniques which originated with NMR in the 1970s have been extended over the past 15 years to the optical regime. NMR spectroscopists have developed methods for the design of pulse sequences that resolve otherwise congested spectra, enhance selected spectral features and reveal desired dynamical events. The major experimental and computational advances required for extending these ideas to study electronic and vibrational motions on the femtosecond timescale will be surveyed. The response of complex molecules and semiconductor nanostructures to sequences of optical pulses provides snapshots of their structure and dynamical processes. Two-dimensional correlation plots of the signals show characteristic cross-peak patterns which carry information about hydrogen bonding, secondary structure fluctuations of proteins and amyloid fibrils, and coherent and incoherent energy and charge transfer in photosynthetic complexes. Double quantum coherence signals that are induced by correlations among electrons or excitons allow the visualization of correlated wavefunctions. Future extensions to the attosecond regime using xray pulses will be discussed. Since core excitations are highly localized at selected atoms, such signals can monitor the motions of valence electron wavepackets in real space with atomic spatial resolution. Common principles underlying coherent spectroscopy techniques for spins, valence electrons, and core electronic excitations, spanning frequencies from radiowaves, infrared, ultraviolet all the way to hard X-rays will be discussed. [4pt] [1] "Coherent Multidimensional Optical Probes for Electronic Correlations and Exciton Dynamics; from NMR to X-rays", S. Mukamel, D. Abramavicius, L. Yang, W.Zhuang, I.V. Schweigert and D. Voronine. Acct.Chem.Res. Acct.Chem.Res. 42, 553-562 (2009). [0pt] [2] "Coherent Multidimensional Optical Spectroscopy Excitons in Molecular Aggregates; Quasiparticle vs. Supermolecule Perspectives", D. Abramavicius, B. Palmieri, D. Voronine, F. Sanda and S. Mukamel, Chem. Rev. 109, 2350-2408 (2009).

Mukamel, Shaul

2011-03-01

252

Elastic properties, Young's modulus determination and structural stability of the tropocollagen molecule: a computational study by steered molecular dynamics.  

PubMed

The aim of this report is to investigate at microscopic level the elastic properties of a tropocollagen-like molecule submitted to linear traction along its longitudinal axis. For this purpose, we performed steered molecular dynamics (SMD) simulations for a wide range of spring constants in order to test the molecular response based on a two-spring model connected in series. An elastic behavior was observed in an elongation range of 2.5-4% of the molecular length, estimating an "effective molecular elastic constant" of 1.02+/-0.20 kcal/mol A2 in this region. Accordingly, a Young's modulus for the tropocollagen molecule of Y=4.8+/-1.0 GPa was calculated. The complex hydrogen bond network was traced along molecular dynamics (MD) and SMD simulations revealing a rearrangement of these interactions preserving the integrity of the molecular structure when submitted to traction. No evidence of the significant role attributed to water bridges for structural stability was detected, on the contrary facts pointed out that the hydrogen bond network might be the responsible. PMID:15922764

Lorenzo, Alicia Claudia; Caffarena, Ernesto Raúl

2005-07-01

253

Pattern recognition analysis in complex molecule synthesis and the preparation of iso-Diels-Alder motifs.  

PubMed

The identification of synthesizable substructural domains within more complex structural targets is of significant value in designing a workable plan of synthesis. We term this process "pattern recognition analysis" (PRA). In this paper we continued to build on the theme of PRA as a potential resource in retrosynthetic blueprints to reach highly challenging targets. The paper operates at two levels. First, there is provided a clear sense of definitions of categories by which patterns are related to hypothetical reaction types. Although the required reaction type may for the moment not exist, we believe that this method of analysis is likely to promote innovation that identifies unmet needs and opportunities to advance the cause of complex target synthesis. In addition, we describe reductions to practice in expanding the menu of achievable patterns. It is likely that the future value of PRA will be associated with its utility in leading the way to new and exploitable chemical innovation. PMID:23784777

Peng, Feng; Grote, Robin E; Wilson, Rebecca M; Danishefsky, Samuel J

2013-06-19

254

Dynamical behavior of one-dimensional water molecule chains in zeolites: Nanosecond time-scale molecular dynamics simulations of bikitaite  

NASA Astrophysics Data System (ADS)

Nanosecond scale molecular dynamics simulations of the behavior of the one-dimensional water molecule chains adsorbed in the parallel nanochannels of bikitaite, a rare lithium containing zeolite, were performed at different temperatures and for the fully and partially hydrated material. New empirical potential functions have been developed for representing lithium-water interactions. The structure and the vibrational spectrum of bikitaite were in agreement both with experimental data and Car-Parrinello molecular dynamics results. Classical molecular dynamics simulations were extended to the nanosecond time scale in order to study the flip motion of water molecules around the hydrogen bonds connecting adjacent molecules in the chains, which has been observed by NMR experiments, and the dehydration mechanism at high temperature. Computed relaxation times of the flip motion follow the Arrhenius behavior found experimentally, but the activation energy of the simulated system is slightly underestimated. Based on the results of the simulations, it may be suggested that the dehydration proceeds by a defect-driven stepwise diffusion. The diffusive mechanism appears as a single-file motion: the molecules never pass one another, even at temperatures as high as about 1000 K, nor can they switch between different channels. However, the mean square displacement (MSD) of the molecules, computed with respect to the center of mass of the simulated system, shows an irregular trend from which the single-file diffusion cannot be clearly evidenced. If the MSDs are evaluated with respect to the center of mass of the molecules hosted in each channel, the expected dependence on the square root of time finally appears.

Demontis, Pierfranco; Stara, Giovanna; Suffritti, Giuseppe B.

2004-05-01

255

Rotational fluctuation of molecules in quantum clusters. II. Molecular rotation and superfluidity in OCS-doped helium-4 clusters.  

PubMed

In this paper, quantum fluctuations of a carbonyl sulfide molecule in helium-4 clusters are studied as a function of cluster size N in a small-to-large size regime (2molecular rotation of the dopant shows nonmonotonic size dependence in the range of 10molecule. The size dependence on the rotational constant shows a plateau for N>or=20, which is larger than the experimental nanodroplet value. Superfluid response of the doped cluster is found to show remarkable anisotropy especially for Nmolecular axis shows a steep increase at N=10, giving the significant enhancement of the rotational fluctuation of the molecule. On the other hand, the superfluid fraction regarding the axis parallel to the molecular axis reaches 0.9 at N=5, arising from the bosonic exchange cycles of the helium atoms around the molecular axis. The anisotropy in the superfluid response is found to be the direct consequence of the configurations of the bosonic exchange cycles. PMID:17381208

Miura, Shinichi

2007-03-21

256

Rotational fluctuation of molecules in quantum clusters. II. Molecular rotation and superfluidity in OCS-doped helium-4 clusters  

SciTech Connect

In this paper, quantum fluctuations of a carbonyl sulfide molecule in helium-4 clusters are studied as a function of cluster size N in a small-to-large size regime (2{<=}N{<=}64). The molecular rotation of the dopant shows nonmonotonic size dependence in the range of 10{<=}N{<=}20, reflecting the density distribution of the helium atoms around the molecule. The size dependence on the rotational constant shows a plateau for N{>=}20, which is larger than the experimental nanodroplet value. Superfluid response of the doped cluster is found to show remarkable anisotropy especially for N{<=}20. The superfluid fraction regarding the axis perpendicular to the molecular axis shows a steep increase at N=10, giving the significant enhancement of the rotational fluctuation of the molecule. On the other hand, the superfluid fraction regarding the axis parallel to the molecular axis reaches 0.9 at N=5, arising from the bosonic exchange cycles of the helium atoms around the molecular axis. The anisotropy in the superfluid response is found to be the direct consequence of the configurations of the bosonic exchange cycles.

Miura, Shinichi [Institute for Molecular Science, 38 Myodaiji, Okazaki 444-8585 (Japan)

2007-03-21

257

A molecular dynamics study of the swelling patterns of Na/Cs-montmorillonites and the hydration of interlayer cations  

NASA Astrophysics Data System (ADS)

We report on a molecular dynamics study of the swelling patterns of an Na-rich/Cs-poor montomorillonite and a Cs-montomorillonite. The recently developed CLAYFF force field is used to predict the basal spacing as a function of the water content in the interlayer. The simulations reproduce the swelling patterns of the Na and Cs-montomorillonite, suggesting a mechanism of its hydration different from that of the montomorillonite. In addition, we find that the differences in size and hydration energy of Na and Cs ions have strong implications for the structure and the internal energy of interlayer water. In particular, our results indicate that the hydrate difference in the presence of coexistent Na and Cs has a larger influence on the behavior of a clay—water system. For Na-rich/Cs-poor montomorillonite, the hydration energy values of Na ions and water molecules each have a dramatic increase compared with those in Na-montomorillonite on the interlayer spacing, and the hydration energy values of Cs ions and water molecules decrease somewhat compared with those in Cs-montomorillonite.

Liu, Tao; Chen, Yu-Qing

2013-02-01

258

Electronic transport in biphenyl single-molecule junctions with carbon nanotubes electrodes: The role of molecular conformation and chirality  

SciTech Connect

We investigate, by means of ab initio calculations, electronic transport in molecular junctions composed of a biphenyl molecule attached to metallic carbon nanotubes. We find that the conductance is proportional to cos{sup 2} {theta}, with {theta} the angle between phenyl rings, when the Fermi level of the contacts lies within the frontier molecular orbitals energy gap. This result, which agrees with experiments in biphenyl junctions with nonorganic contacts, suggests that the cos{sup 2} {theta} law has a more general applicability, irrespective of the nature of the electrodes. We calculate the geometrical degree of chirality of the junction, which only depends on the atomic positions, and demonstrate that it is not only proportional to cos{sup 2} {theta} but also is strongly correlated with the current through the system. These results indicate that molecular conformation plays the preponderant role in determining transport properties of biphenyl-carbon nanotubes molecular junctions.

Brito Silva, C. A. Jr.; Granhen, E. R. [Pos-Graduacao em Engenharia Eletrica, Universidade Federal do Para, 66075-900 Belem, PA (Brazil); Silva, S. J. S. da; Leal, J. F. P. [Pos-Graduacao em Fisica, Universidade Federal do Para, 66075-110 Belem, PA (Brazil); Del Nero, J. [Departamento de Fisica, Universidade Federal do Para, 66075-110 Belem, PA (Brazil); Divisao de Metrologia de Materiais, Instituto Nacional de Metrologia, Normalizacao e Qualidade Industrial, 25250-020 Duque de Caxias, RJ (Brazil); Instituto de Fisica, Universidade Federal do Rio de Janeiro, 21941-972 Rio de Janeiro, RJ (Brazil); Pinheiro, F. A. [Instituto de Fisica, Universidade Federal do Rio de Janeiro, 21941-972 Rio de Janeiro, RJ (Brazil)

2010-08-15

259

High-order harmonic generation in diatomic molecules: A quantum-orbit analysis of the interference patterns  

SciTech Connect

We perform a detailed analysis of high-order harmonic generation in diatomic molecules within the strong-field approximation (SFA), with emphasis on quantum-interference effects. Specifically, we investigate how the different types of electron orbits, involving one or two centers, affect the interference patterns in the spectra. We also briefly address the influence of the choice of gauge and of the initial and final electronic bound states on such patterns. For the length-gauge SFA and undressed bound states, there exist additional terms, which can be interpreted as potential energy shifts. If, on the one hand, such shifts alter the potential barriers through which the electron initially tunnels, and may lead to a questionable physical interpretation of the features encountered, on the other hand, they seem to be necessary in order to reproduce the overall maxima and minima in the spectra. Indeed, for dressed electronic bound states in the length gauge, or undressed bound states in the velocity gauge, for which such shifts are absent, there is a breakdown of the interference patterns. In order to avoid such a problem, we provide an alternative pathway for the electron to reach the continuum, by means of an additional attosecond-pulse train. A comparison of the purely monochromatic case with the situation for which the attosecond pulses are present suggests that the patterns are due to the interference between the electron orbits which finish at different centers, regardless of whether one or two centers are involved.

Figueira de Morisson Faria, C. [Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT (United Kingdom)

2007-10-15

260

Molecular patterning mechanism underlying metamorphosis of the thoracic leg in Manduca sexta.  

PubMed

The tobacco hornworm Manduca sexta, like many holometabolous insects, makes two versions of its thoracic legs. The simple legs of the larva are formed during embryogenesis, but then are transformed into the more complex adult legs at metamorphosis. To elucidate the molecular patterning mechanism underlying this biphasic development, we examined the expression patterns of five genes known to be involved in patterning the proximal-distal axis in insect legs. In the developing larval leg of Manduca, the early patterning genes Distal-less and Extradenticle are already expressed in patterns comparable to the adult legs of other insects. In contrast, Bric-a-brac and dachshund are expressed in patterns similar to transient patterns observed during early stages of leg development in Drosophila. During metamorphosis of the leg, the two genes finally develop mature expression patterns. Our results are consistent with the hypothesis that the larval leg morphology is produced by a transient arrest in the conserved adult leg patterning process in insects. In addition, we find that, during the adult leg development, some cells in the leg express the patterning genes de novo suggesting that the remodeling of the leg involves changes in the patterning gene regulation. PMID:17418115

Tanaka, Kohtaro; Truman, James W

2007-03-06

261

Towards redistribution laser cooling of molecular gases: production of candidtate molecules SrH by laser ablation  

NASA Astrophysics Data System (ADS)

Laser cooling by collisional redistribution of radiation has been successfully applied in the past for cooling dense atomic gases. Here we report on progress of work aiming at the demonstration of redistribution laser cooling in a molecular gas. The candidate molecule strontium monohydride is produced by laser ablation of strontium dihydride in a pressurized noble gas atmosphere. The composition of the ablation plasma plume is analyzed by measuring its emission spectrum. The dynamics of SrH molecular density following the ablation laser pulse is studied as a function of the buffer gas pressure and the laser intensity.

Simon, P.; Moroshkin, P.; Weller, L.; Saß, A.; Weitz, M.

2013-03-01

262

Synthesis and Magnetism of High Curie Temperature Prussian Blue Analogue Molecular Nanomagnet-Chromium Cyanide Molecule Nanowire Arrays  

NASA Astrophysics Data System (ADS)

The goal to synthesize molecular nanomagnets that exhibit spontaneous magnetic ordering close to room temperature might enable one to apply them in the fields of magnetic memory devices and microelectronics. Chromium cyanide molecule nanowire arrays with diameters of about 50 nm and lengths up to 4?m have been synthesized by an electrodepositing technology based on anodizing anodic aluminum oxide films. Characterization measurements show that the oxidation state of the chromium ions in the chromium cyanide nanowires can be expressed as Cr^3+--CN--Cr^3+. Magnetic properties measurements indicate that the Curie temperature of chromium cyanide nanowire is 200 K, which is closer room temperature compared with current molecular nanomagnet systems.

Zhou, Pingheng; Xue, Desheng; Yao, Jinli

2009-03-01

263

Molecular--cytogenetic characterization of the Vicia faba genome -- heterochromatin differentiation, replication patterns and sequence localization  

Microsoft Academic Search

A comprehensive survey of the molecular--cytogenetic features of the Vicia faba chromosome complement (2n = 12) is given. It includes previous as well as new original data. Various Giemsa, restriction endonuclease and fluorochrome banding patterns, azacytidine-mediated segment extension, replication patterns, lateral A\\/T asymmetry and sequence localization data for tandemly arranged simple sequence repeats, dispersed repeats and coding sequences as well

Jorg Fuchs; Sabine Strehl; Andrea Brandes; Dieter Schweizer; Ingo Schubert

1998-01-01

264

Resonance enhanced multiphoton ionization spectra of molecules and molecular fragments. Annual technical report, March 1991--February 1992  

SciTech Connect

Resonance Enhanced Multiphoton Ionization (REMPI) utilizes pulsed laser radiation to prepare a molecule in an excited state via absorption of one or more photons and to subsequently ionize that state before it can decay. The overall objective of this effort is to carry out theoretical studies of these REMPI processes in molecules and molecular fragments which are designed to provide a robust analysis and prediction of key spectral features of interest in several experimental studies and applications of this technique. A specific and very important objective of the effort is to predict the vibrational and rotational ion distributions which result from REMPI of representative molecules and to understand the underlying mechanisms that give use to these ion distributions. The author highlights progress made during this period.

NONE

1993-12-31

265

RNA templating of molecular assembly and covalent modification patterning in early molecular evolution and modern biosystems  

Microsoft Academic Search

The Direct RNA Template (DRT) hypothesis proposes that an early stage of genetic code evolution involved RNA molecules acting as stereochemical recognition templates for assembly of specific amino acids in sequence-ordered arrays, providing a framework for directed covalent peptide bond formation. It is hypothesized here that modern biological precedents may exist for RNA-based structural templating with functional analogies to hypothetical

Ian S. Dunn

2011-01-01

266

Molecular Zeeman and Natural Vibrational Optical Activity Studies of Selected Molecules  

Microsoft Academic Search

This thesis consists of two independent parts in the field of vibrational optical activity. Part I describes the magnetic vibrational circular dichroism (MVCD) studies of some small molecules in the gas phase and the fullerenes in solution while Part II presents experimental work on the natural vibrational circular dichroism (VCD) and Raman optical activity (ROA) of some medium-sized organic molecules.

Cheok Neng Tam

1996-01-01

267

Statistical mechanics of deformable molecular liquids: Thermal expansion and isomerization of diatomic molecules  

NASA Astrophysics Data System (ADS)

Equilibrium two-body correlations in liquids composed of deformable molecules are formulated with use of the density-functional theory and the interaction site formalism. As applications, we study two model systems, liquid nitrogen and simplified liquid n butane, in which each molecule has two stable bond lengths. The latter may be considered as a toy model to study conformational equilibrium.

Munakata, Toyonori; Yoshida, Shuhei; Hirata, Fumio

1996-10-01

268

Dynamical coupling and negative differential resistance from interactions across the molecule-electrode interface in molecular junctions.  

PubMed

Negative differential resistance - a decrease in current with increasing bias voltage - is a counter-intuitive effect that is observed in various molecular junctions. Here, we present a novel mechanism that may be responsible for such an effect, based on strong Coulomb interaction between electrons in the molecule and electrons on the atoms closest to the molecule. The Coulomb interaction induces electron-hole binding across the molecule-electrode interface, resulting in a renormalized and enhanced molecule-electrode coupling. Using a self-consistent non-equilibrium Green's function approach, we show that the effective coupling is non-monotonic in bias voltage, leading to negative differential resistance. The model is in accord with recent experimental observations that showed a correlation between the negative differential resistance and the coupling strength. We provide detailed suggestions for experimental tests which may help to shed light on the origin of the negative differential resistance. Finally, we demonstrate that the interface Coulomb interaction affects not only the I-V curves but also the thermoelectric properties of molecular junctions. PMID:24160536

Dubi, Yonatan

2013-10-21

269

Dynamical coupling and negative differential resistance from interactions across the molecule-electrode interface in molecular junctions  

NASA Astrophysics Data System (ADS)

Negative differential resistance - a decrease in current with increasing bias voltage - is a counter-intuitive effect that is observed in various molecular junctions. Here, we present a novel mechanism that may be responsible for such an effect, based on strong Coulomb interaction between electrons in the molecule and electrons on the atoms closest to the molecule. The Coulomb interaction induces electron-hole binding across the molecule-electrode interface, resulting in a renormalized and enhanced molecule-electrode coupling. Using a self-consistent non-equilibrium Green's function approach, we show that the effective coupling is non-monotonic in bias voltage, leading to negative differential resistance. The model is in accord with recent experimental observations that showed a correlation between the negative differential resistance and the coupling strength. We provide detailed suggestions for experimental tests which may help to shed light on the origin of the negative differential resistance. Finally, we demonstrate that the interface Coulomb interaction affects not only the I-V curves but also the thermoelectric properties of molecular junctions.

Dubi, Yonatan

2013-10-01

270

In vitro motility assays and single molecule analyses reveal functional structural transitions in the molecular motor myosin  

NASA Astrophysics Data System (ADS)

The molecular basis of how myosin motors work has been significantly advanced by laser trap and other single molecule studies of myosins V and VI. Myosin V moves processively by stepping arm-over-arm, walking along the 36-nm pseudo-repeat of an actin filament by swinging its long lever arms through an angle of ˜70 ^o, and hydrolyzing one ATP per step. Compared to the laser trap, we have improved time resolution to submilliseconds by tracking single gold nanoparticle-myosin V conjugates using darkfield imaging, and have directly observed the behavior of the unbound head as the motor translocates. We have also developed a technique called single-molecule high resolution co-localization (SHREC), which allows simultaneous co-localization of two chromatically differing fluorophores only 10 nm apart. We used SHREC to directly observe myosin V molecules walking hand-over-hand. Myosin VI, a considerably different myosin family member, has been the biggest challenge to the lever arm hypothesis of myosin movement. It has a very short light chain binding domain (the conventional lever arm). Nevertheless, the molecule surprisingly steps processively 36 nm along an actin filament. Furthermore, myosin VI moves in the opposite direction to that of myosin II and myosin V. We now understand how this marvelous molecular motor achieves these feats.

Spudich, James

2010-03-01

271

Effect of surrounding gas on velocity distribution function of molecules in molecular beam  

Microsoft Academic Search

Molecular-beam methods have become widely used in recent times for the study of flows of rarefied gases [1]. However, the very first experiments with molecular beams for agasdynamic source [2] showed that the measured intensities fell below theoretical predictions. Most devices for the creation of a molecular beam by means of a gasdynamic source have pumping equipment of comparatively low

A. E. Zarvin; R. G. Sharafutdinov

1976-01-01

272

Luminescences of Pyrene Single Crystal and Pyrene Molecules Inserted in a Molecular Vessel of Cyclodextrin  

NASA Astrophysics Data System (ADS)

Highly purified single crystals of pyrene were made by a gas phase crystal growth method from 180 times of zone-refined pyrene. The dry powder of ?-cyclodextrin including a pyrene single molecule and that of ?-cyclodextrin including twin molecules were prepared under vacuum. The luminescence spectra of pyrene single molecules, twin molecules and single crystals, and their temperature dependences were measured with great care in the process of cooling the samples. It is found that the features of luminescence spectra at 2 K are quite different from each other. Pyrene twin molecules in ?-cyclodextrin show an excimer luminescence similar to that of single crystal. The vibronic luminescence in the range of 3.0-3.5 eV comes from the ground-excited-state complex, or in other words, from the vibronic exciton, in contrast to the hitherto-assigned luminescence from another type of selftrapped exciton or metastable B-state which is the precursor of selftrapped excitons.

Takahashi, Nobuaki; Gombojav, Bold; Yoshinari, Takehisa; Takahashi, Yoshio; Nagasaka, Shin-ichiro; Yamamoto, Aishi; Goto, Takenari; Kasuya, Atsuo

2007-03-01

273

Enumerating molecules.  

SciTech Connect

This report is a comprehensive review of the field of molecular enumeration from early isomer counting theories to evolutionary algorithms that design molecules in silico. The core of the review is a detail account on how molecules are counted, enumerated, and sampled. The practical applications of molecular enumeration are also reviewed for chemical information, structure elucidation, molecular design, and combinatorial library design purposes. This review is to appear as a chapter in Reviews in Computational Chemistry volume 21 edited by Kenny B. Lipkowitz.

Visco, Donald Patrick, Jr. (, . Tennessee Technological University, Cookeville, TN); Faulon, Jean-Loup Michel; Roe, Diana C.

2004-04-01

274

Bench-to-bedside review: Damage-associated molecular patterns in the onset of ventilator-induced lung injury  

PubMed Central

Mechanical ventilation (MV) has the potential to worsen pre-existing lung injury or even to initiate lung injury. Moreover, it is thought that injurious MV contributes to the overwhelming inflammatory response seen in patients with acute lung injury or acute respiratory distress syndrome. Ventilator-induced lung injury (VILI) is characterized by increased endothelial and epithelial permeability and pulmonary inflammation, in which the innate immune system plays a key role. A growing body of evidence indicates that endogenous danger molecules, also termed damage-associated molecular patterns (DAMPs), are released upon tissue injury and modulate the inflammatory response. DAMPs activate pattern recognition receptors, may induce the release of proinflammatory cytokines and chemokines, and have been shown to initiate or propagate inflammation in non-infectious conditions. Experimental and clinical studies demonstrate the presence of DAMPs in bronchoalveolar lavage fluid in patients with VILI and the upregulation of pattern recognition receptors in lung tissue by MV. The objective of the present article is to review research in the area of DAMPs, their recognition by the innate immune system, their role in VILI, and the potential utility of blocking DAMP signaling pathways to reduce VILI in the critically ill.

2011-01-01

275

In situ metallization of patterned polymer brushes created by molecular transfer print and fill.  

PubMed

A chemical pattern consisting of end-grafted polystyrene brushes (20 nm lines on a 40 nm pitch) on the native oxide of silicon wafers was defined by molecular transfer printing from assembled block co-polymer films. End-grafted hydroxyl-terminated poly(2-vinyl pyridine) brushes were selectively deposited in the interspatial regions. The poly(2-vinyl pyridine) regions selectively sequester acidic HAuCl4 from solution and form arrays of small Au nanoparticles upon exposure to oxygen plasma within the confines of the macromolecular brush layer. This print and fill process to pattern polymer brushes is a generalizable strategy to create functional chemical surface patterns. PMID:23518622

Thode, Christopher J; Cook, Peter L; Jiang, Yaming; Serdar Onses, M; Ji, Shengxiang; Himpsel, Franz J; Nealey, Paul F

2013-03-22

276

Proteomic analysis of ganglioside-associated membrane molecules: substantial basis for molecular clustering.  

PubMed

Ganglioside GD3 is specifically expressed in human melanomas, and plays a role in the enhancement of malignant phenotypes of melanoma cells. To analyze the mechanisms by which GD3 enhances malignant properties and signals in melanomas, it is essential to clarify how GD3 interacts with membrane molecules on the cell membrane. In this study, we performed proteomics analysis of glycolipid-enriched microdomains (GEM) with current sucrose density gradient ultracentrifugation of Triton X-100 extracts and MS. We also examined GD3-associated molecules using enzyme-mediated activation of radical sources (EMARS) reaction combined with MS. Comparison of molecules identified as residents in GEM/rafts and those detected by EMARS reaction using an anti-GD3 antibody revealed that a relatively low number of molecules is recruited around GD3, while a number of membrane and secreted molecules was defined in GEM/rafts. These results suggested that EMARS reaction is useful to identify actually interacting molecules with gangliosides such as GD3 on the cell membrane, and many other microdomains than GD3-associating rafts exist. Representative examples of GD3-associated molecules such as neogenin and MCAM were shown. PMID:22936677

Hashimoto, Noboru; Hamamura, Kazunori; Kotani, Norihiro; Furukawa, Keiko; Kaneko, Kei; Honke, Koichi; Furukawa, Koichi

2012-10-01

277

A molecular dynamics study of Hras-GTP and GDP complexes: The properties of water molecules around guanine nucleotide  

NASA Astrophysics Data System (ADS)

We study the structures of Hras-GTP and Hras-GDP complexes in water in order to investigate the mechanism of hydrolysis of GTP in the Hras-GTP complex. Understanding of the mechanism of hydrolysis of GTP in the Hras-GTP complex plays a key role in overcoming the human cancer. We performed molecular dynamics (MD) simulations of Hras-GTP complex and Hras-GDP complex in water using AMBER03 parameters and our calculated parameters around Mg2+. Using the trajectories of the MD simulations, we calculated the radial distribution functions of water molecules around the phosphorus atoms in guanine nucleotide in each complex. We also calculated the radius of the first hydration sphere, the averaged number of water molecules in the first hydration sphere, and the distribution of duration time of water molecules in the first hydration sphere. We also calculated the distribution of water molecules with respect to the angle around the PG in GTP and PB in GDP. It is suggested that the hydrolysis is triggered by water molecules attacking ?-phosphate from the direction rotated 35° to the O1B from the axis defined by PG and O3B.

Miyakawa, T.; Morikawa, R.; Takasu, M.; Sugimori, K.; Kawaguchi, K.; Saito, H.; Nagao, H.

2013-02-01

278

Pathogen-associated molecular pattern-induced mitochondrial membrane depolarization in the earthworm Eisenia hortensis  

Microsoft Academic Search

Innate immune responses of the earthworm Eisenia hortensis were studied by detecting mitochondrial membrane depolarization and reactive oxygen species (ROS) production after incubation with pathogen-associated molecular patterns (PAMPs). Coelomocytes from E. hortensis were incubated with zymosan, flagellin, or peptidoglycan (PTG) for 48h in vitro and studied using flow cytometric assays for changes in mitochondrial membrane potential (??m) or ROS production

Timothy Nacarelli; Sheryl L. Fuller-Espie

2011-01-01

279

Highly consistent patterns for inherited human diseases at the molecular level  

Microsoft Academic Search

Over 1600 mammalian genes are known to cause an inherited dis- order, when subjected to one or more mutations. These disease genes represent a unique resourcefor the identification and quantifica- tionofrelationships between phenotypic attributesof adiseaseandthe molecular features of the associated disease genes, including their ascribed annotated functional classes and expression patterns. Such analyses can provide a more global perspective and

Núria López-bigas; Benjamin J. Blencowe; Christos A. Ouzounis

2006-01-01

280

LARGE SCALE EVALUATION OF A PATTERN RECOGNITION/EXPERT SYSTEM FOR MASS SPECTRAL MOLECULAR WEIGHT ESTIMATION  

EPA Science Inventory

A fast, personal-computer based method of estimating molecular weights of organic compounds from low resolution mass I spectra has been thoroughly evaluated. he method is based on a rule-based pattern,recognition/expert system approach which uses empirical linear corrections whic...

281

Calculating Structures and Free Energies of Complex Molecules:  Combining Molecular Mechanics and Continuum Models  

Microsoft Academic Search

A historical perspective on the application of molecular dynamics (MD) to biological macromolecules is presented. Recent develop- ments combining state-of-the-art force fields with continuum solvation calculations have allowed us to reach the fourth era of MD applications in which one can often derive both accurate structure and accurate relative free energies from molecular dynam- ics trajectories. We illustrate such applications

Peter A. Kollman; Irina Massova; Carolina Reyes; Bernd Kuhn; Shuanghong Huo; Lillian Chong; Matthew Lee; Taisung Lee; Yong Duan; Wei Wang; Oreola Donini; Piotr Cieplak; Jaysharee Srinivasan; David A. Case; Thomas E. Cheatham

2000-01-01

282

Capturing molecules with templated materials—Analysis and rational design of molecularly imprinted polymers  

Microsoft Academic Search

The creation of synthetic tailor-made receptors capable of recognizing desired molecular targets with high affinity and selectivity is a persistent long-term goal for researchers in the fields of chemical, biological, and pharmaceutical research. Compared to biomacromolecular receptors, these synthetic receptors promise simplified production and processing, less costs, and more robust receptor architectures. During recent decades, molecularly imprinted polymers (MIPs) are

Shuting Wei; Michael Jakusch; Boris Mizaikoff

2006-01-01

283

Movies of molecular motions and reactions: the single-molecule, real-time transmission electron microscope imaging technique.  

PubMed

"The truth is, the Science of Nature has been already too long made only a work of the Brain and the Fancy: It is now high time that it should return to the plainness and soundness of Observations on material and obvious things," proudly declared Robert Hooke in his highly successful picture book of microscopic and telescopic images, "Micrographia" in 1665. Hooke's statement has remained true in chemistry, where a considerable work of the brain and the fancy is still necessary. Single-molecule, real-time transmission electron microscope (SMRT-TEM) imaging at an atomic resolution now allows us to learn about molecules simply by watching movies of them. Like any dream come true, the new analytical technique challenged the old common sense of the communities, and offers new research opportunities that are unavailable by conventional methods. With its capacity to visualize the motions and the reactions of individual molecules and molecular clusters, the SMRT-TEM technique will become an indispensable tool in molecular science and the engineering of natural and synthetic substances, as well as in science education. PMID:23280645

Nakamura, Eiichi

2012-12-17

284

Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations.  

PubMed

RNA molecules are stabilized by a wide range of noncanonical interactions that are not present in DNA. Among them, the recently classified base-phosphate (BPh) interactions belong to the most important ones. Twelve percent of nucleotides in the ribosomal crystal structures are involved in BPh interactions. BPh interactions are highly conserved and provide major constraints on RNA sequence evolution. Here we provide assessment of the energetics of BPh interactions using MP2 computations extrapolated to the complete basis set of atomic orbitals and corrected for higher-order electron correlation effects. The reference computations are compared with DFT-D and DFT-D3 approaches, the SAPT method, and the molecular mechanics force field. The computations, besides providing the basic benchmark for the BPh interactions, allow some refinements of the original classification, including identification of some potential doubly bonded BPh patterns. The reference computations are followed by analysis of some larger RNA fragments that consider the context of the BPh interactions. The computations demonstrate the complexity of interaction patterns utilizing the BPh interactions in real RNA structures. The BPh interactions are often involved in intricate interaction networks. We studied BPh interactions of protonated adenine that can contribute to catalysis of hairpin ribozyme, the key BPh interaction in the S-turn motif of the sarcin-ricin loop, which may predetermine the S-turn topology and complex BPh patterns from the glmS riboswitch. Finally, the structural stability of BPh interactions in explicit solvent molecular dynamics simulations is assessed. The simulations well preserve key BPh interactions and allow dissection of structurally/functionally important water-meditated BPh bridges, which could not be considered in earlier bioinformatics classification of BPh interactions. PMID:21910417

Zgarbová, Marie; Jure?ka, Petr; Banáš, Pavel; Otyepka, Michal; Sponer, Judit E; Leontis, Neocles B; Zirbel, Craig L; Sponer, Ji?í

2011-09-12

285

Sialyllactose in Viral Membrane Gangliosides Is a Novel Molecular Recognition Pattern for Mature Dendritic Cell Capture of HIV-1  

PubMed Central

HIV-1 is internalized into mature dendritic cells (mDCs) via an as yet undefined mechanism with subsequent transfer of stored, infectious virus to CD4+ T lymphocytes. Thus, HIV-1 subverts a DC antigen capture mechanism to promote viral spread. Here, we show that gangliosides in the HIV-1 membrane are the key molecules for mDC uptake. HIV-1 virus-like particles and liposomes mimicking the HIV-1 lipid composition were shown to use a common internalization pathway and the same trafficking route within mDCs. Hence, these results demonstrate that gangliosides can act as viral attachment factors, in addition to their well known function as cellular receptors for certain viruses. Furthermore, the sialyllactose molecule present in specific gangliosides was identified as the determinant moiety for mDC HIV-1 uptake. Thus, sialyllactose represents a novel molecular recognition pattern for mDC capture, and may be crucial both for antigen presentation leading to immunity against pathogens and for succumbing to subversion by HIV-1.

Contreras, F.-Xabier; Rodriguez-Plata, Maria T.; Glass, Barbel; Erkizia, Itziar; Prado, Julia G.; Casas, Josefina; Fabrias, Gemma; Krausslich, Hans-Georg; Martinez-Picado, Javier

2012-01-01

286

Extended molecular Ornstein-Zernike integral equation for fully anisotropic solute molecules: Formulation in a rectangular coordinate system  

NASA Astrophysics Data System (ADS)

An extended molecular Ornstein-Zernike (XMOZ) integral equation is formulated to calculate the spatial distribution of solvent around a solute of arbitrary shape and solid surfaces. The conventional MOZ theory employs spherical harmonic expansion technique to treat the molecular orientation of components of solution. Although the MOZ formalism is fully exact analytically, the truncation of the spherical harmonic expansion requires at a finite order for numerical calculation and causes the significant error for complex molecules. The XMOZ integral equation is the natural extension of the conventional MOZ theory to a rectangular coordinate system, which is free from the truncation of spherical harmonic expansion with respect to solute orientation. In order to show its applicability, we applied the XMOZ theory to several systems using the hypernetted-chain (HNC) and Kovalenko-Hirata approximations. The quality of results obtained within our theory is discussed by comparison with values from the conventional MOZ theory, molecular dynamics simulation, and three-dimensional reference interaction site model theory. The spatial distributions of water around the complex of non-charged sphere and dumbbell were calculated. Using this system, the approximation level of the XMOZ and other methods are discussed. To assess our theory, we also computed the excess chemical potentials for three realistic molecules (water, methane, and alanine dipeptide). We obtained the qualitatively reasonable results by using the XMOZ/HNC theory. The XMOZ theory covers a wide variety of applications in solution chemistry as a useful tool to calculate solvation thermodynamics.

Ishizuka, Ryosuke; Yoshida, Norio

2013-08-01

287

Extended molecular Ornstein-Zernike integral equation for fully anisotropic solute molecules: Formulation in a rectangular coordinate system.  

PubMed

An extended molecular Ornstein-Zernike (XMOZ) integral equation is formulated to calculate the spatial distribution of solvent around a solute of arbitrary shape and solid surfaces. The conventional MOZ theory employs spherical harmonic expansion technique to treat the molecular orientation of components of solution. Although the MOZ formalism is fully exact analytically, the truncation of the spherical harmonic expansion requires at a finite order for numerical calculation and causes the significant error for complex molecules. The XMOZ integral equation is the natural extension of the conventional MOZ theory to a rectangular coordinate system, which is free from the truncation of spherical harmonic expansion with respect to solute orientation. In order to show its applicability, we applied the XMOZ theory to several systems using the hypernetted-chain (HNC) and Kovalenko-Hirata approximations. The quality of results obtained within our theory is discussed by comparison with values from the conventional MOZ theory, molecular dynamics simulation, and three-dimensional reference interaction site model theory. The spatial distributions of water around the complex of non-charged sphere and dumbbell were calculated. Using this system, the approximation level of the XMOZ and other methods are discussed. To assess our theory, we also computed the excess chemical potentials for three realistic molecules (water, methane, and alanine dipeptide). We obtained the qualitatively reasonable results by using the XMOZ/HNC theory. The XMOZ theory covers a wide variety of applications in solution chemistry as a useful tool to calculate solvation thermodynamics. PMID:24006986

Ishizuka, Ryosuke; Yoshida, Norio

2013-08-28

288

Direct observation of molecularly-aligned molecules in the second physisorbed layer-CO/Ag(110)  

SciTech Connect

We report the direct observation of oriented second-layer physisorbed molecules on a single crystal surface by electron stimulated desorption. Experiments and simulations show that the orientation of the second-layer physisorbed CO molecules on Ag(110) is the result of both electrostatic and dispersion forces from the underlying chemisorbed CO and Ag atoms. At 25 K, the physisorbed C-O bond is tilted and azimuthally oriented with the C-O bond axis inclined in an azimuthal plane at 45° to the principal Ag( 110) azimuthal crystallographic directions. The O atom in CO is directed outward, giving an O+ beam at 43° to the normal.

Lee, J.-G. (Chevron Science Center, Pittsburgh, PA); Hong, S.-H. (Chevron Science Center, Pittsburgh, PA); Ahner, J. (Chevron Science Center, Pittsburgh, PA); Zhao, X. (Univ. of Pittsburgh, PA); Chen, L.; Johnson, J.K.; Yates, J.T., Jr. (Chevron Science Center, Pittsburgh, PA)

2006-01-25

289

Application of the dressed-bound-state molecular strong-field approximation to above-threshold ionization of heteronuclear molecules: NO vs. CO.  

PubMed

We theoretically investigate high-order above-threshold ionization (HATI) of heteronuclear diatomic molecules applying the molecular strong-field approximation which includes dressing of the molecular bound state. We consider HATI of nitrogen monoxide molecules, which are characterized by the ? symmetry of their highest occupied molecular orbital. We show that the HATI spectra of NO exhibit characteristic interference structures. We analyze the differences and similarities of the HATI spectra of NO molecules and the spectra of CO (? symmetry) and O(2) (?(g) symmetry) molecules. The symmetry properties of the molecular HATI spectra governed by linearly and elliptically polarized fields are considered in detail. The yields of high-energy electrons, contributing to the plateau region of the photoelectron spectra, strongly depend on the employed ellipticity. PMID:23039599

Busuladži?, M; Hasovi?, E; Becker, W; Miloševi?, D B

2012-10-01

290

Pattern recognition proteins in Manduca sexta plasma  

Microsoft Academic Search

Recognition of nonself is the first step in mounting immune responses. In the innate immune systems of both vertebrates and arthropods, such recognition, termed pattern recognition, is mediated by a group of proteins, known as pattern recognition proteins or receptors. Different pattern recognition proteins recognize and bind to molecules (molecular patterns) present on the surface of microorganisms but absent from

X.-Q. Yu; Y.-F. Zhu; C. Ma; J. A. Fabrick; M. R. Kanost

2002-01-01

291

Design and development of a field-deployable single-molecule detector (SMD) for the analysis of molecular markers†  

PubMed Central

Single-molecule detection (SMD) has demonstrated some attractive benefits for many types of biomolecular analyses including enhanced processing speed by eliminating processing steps, elimination of ensemble averaging and single-molecule sensitivity. However, it's wide spread use has been hampered by the complex instrumentation required for its implementation when using fluorescence as the readout modality. We report herein a simple and compact fluorescence single-molecule instrument that is straightforward to operate and consisted of fiber optics directly coupled to a microfluidic device. The integrated fiber optics served as waveguides to deliver the laser excitation light to the sample and collecting the resulting emission, simplifying the optical requirements associated with traditional SMD instruments by eliminating the need for optical alignment and simplification of the optical train. Additionally, the use of a vertical cavity surface emitting laser and a single photon avalanche diode serving as the excitation source and photon transducer, respectively, as well as a field programmable gate array (FPGA) integrated into the processing electronics assisted in reducing the instrument footprint. This small footprint SMD platform was tested using fluorescent microspheres and single AlexaFluor 660 molecules to determine the optimal operating parameters and system performance. As a demonstration of the utility of this instrument for biomolecular analyses, molecular beacons (MBs) were designed to probe bacterial cells for the gene encoding Gram-positive species. The ability to monitor biomarkers using this simple and portable instrument will have a number of important applications, such as strain-specific detection of pathogenic bacteria or the molecular diagnosis of diseases requiring rapid turn-around-times directly at the point-of-use.

Emory, Jason M.; Peng, Zhiyong; Young, Brandon; Hupert, Mateusz L.; Rousselet, Arnold; Patterson, Donald; Ellison, Brad; Soper, Steven A.

2012-01-01

292

Investigation of multi-state charge-storage properties of redox-active organic molecules in silicon-molecular hybrid devices for DRAM and Flash applications  

Microsoft Academic Search

Molecular electronics has recently spawned a considerable amount of interest with several molecules possessing charge-conduction and charge-storage properties proposed for use in electronic devices. Hybrid silicon-molecular technology has the promise of augmenting the current silicon technology and provide for a transitional path to future molecule-only technology. The focus of this dissertation work has been on developing a class of hybrid

Srivardhan Shivappa Gowda

2007-01-01

293

Tonal Interface to MacroMolecules (TIMMol): A Textual and Tonal Tool for Molecular Visualization  

ERIC Educational Resources Information Center

|We developed the three-dimensional visualization software, Tonal Interface to MacroMolecules or TIMMol, for studying atomic coordinates of protein structures. Key features include audio tones indicating x, y, z location, identification of the cursor location in one-dimensional and three-dimensional space, textual output that can be easily linked…

Cordes, Timothy J.; Carlson, C. Britt; Forest, Katrina T.

2008-01-01

294

Molecular logic with a saccharide probe on the few-molecules level.  

PubMed

In this Communication we describe a two-component saccharide probe with logic capability. The combination of a boronic acid-appended viologen and perylene diimide was able to perform a complementary implication/not implication logic function. Fluorescence quenching and recovery with fructose was analyzed with fluorescence correlation spectroscopy on the level of a few molecules of the reporting dye. PMID:22541028

Elstner, Martin; Weisshart, Klaus; Müllen, Klaus; Schiller, Alexander

2012-05-04

295

Molecular structures of gas-phase polyatomic molecules determined by spectroscopic methods  

Microsoft Academic Search

Spectroscopic data related to the structures of polyatomic molecules in the gas phase have been reviewed, critically evaluated, and compiled. All reported bond distances and angles have been classified as equilibrium (re), average (rz), substitution (rs), or effective (ro) parameters, and have been given a quality rating which is a measure of the parameter uncertainty. The surveyed literature includes work

Marlin D. Harmony; Victor W. Laurie; Robert L. Kuczkowski; R. H. Schwendeman; D. A. Ramsay; Frank J. Lovas; Walter J. Lafferty; Arthur G. Maki

1979-01-01

296

ATOMIC AND MOLECULAR PHYSICS: Lie Algebraic Approach to Energy Transfer for Collinear Collision of Two Anharmonic Diatomic Molecules  

NASA Astrophysics Data System (ADS)

An anharmonic oscillator algebra model is used to study the collinear collisions of two diatomic molecules. The transition probability for vibration-vibration energy transfer is presented. For an application of the method, we talk about the collision of N2+CO, N2+O2, and N2+N2. Through long time averaging, the transition probability changes to the function of total energy of the system. Comparing the results with the quantum results, we can see that the dynamical Lie algebraic method is useful for describing the anharmonic diatomic molecular collision.

Wang, Xiao-Yan; Wang, Peng-Cheng; Qiu, Jian-Feng; Wang, Jin-Xi; Hou, Li-Xia; Xie, Jin-Dong Ding, Shi-Liang

2010-02-01

297

Effect of oat and barley ?-glucans on inhibition of cytokine-induced adhesion molecule expression in human aortic endothelial cells: Molecular structure–function relations  

Microsoft Academic Search

Endothelial cell adhesion molecules have been recognized as an early step in inflammation and atherogenesis. The inhibition of TNF-?-induced expression of vascular cell adhesion molecule (VCAM-1) and intracellular cell adhesion molecule (ICAM-1) in human aortic endothelial cells (HAEC), following pretreatment with mixed-linkage (1?3), (1?4)-?-d-glucans (?-glucans) isolated from oat and barley, and the possible molecular structure–function relations, have been explored. The

Athina Lazaridou; Zoi Papoutsi; Costas G. Biliaderis; Paraskevi Moutsatsou

2011-01-01

298

Pulsed molecular beam scattering of a planar-shaped organic molecule on regularly stepped surfaces of hydrogen-terminated Si(111)  

SciTech Connect

Strong dependence of surface residence time of a planar organic molecule (hydrogen phthalocyanine) on vicinal surfaces of hydrogen-terminated Si(111) was observed in pulsed molecular beam scattering experiments. These results can be explained by the difference in the microscopic contact area of the molecules on the surface, which determines the binding force between the migrating molecules and the surface. The relationship between the observed behavior and the organic thin film growth is discussed.

Shimada, Toshihiro; Ichikawa, Hisashi; Saiki, Koichiro [Department of Chemistry, University of Tokyo, Bunkyo-ku, Tokyo 113-0033 (Japan); Department of Chemistry, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan and Department of Complexity Science and Engineering, University of Tokyo, Kashiwa, Chiba 277-8561 (Japan)

2006-10-02

299

Combined Rietveld-molecular dynamics powder diffraction approach to the location of molecules in porous solids: Application to 1,4-dibromobutane in zeolite Y  

Microsoft Academic Search

X-ray powder diffraction data of zeolite Y were analyzed to reveal the distribution of positions of heavy atoms (Br) of sorbate molecules within the pore system of the zeolite. The complex density distribution obtained was analyzed and interpreted by molecular dynamics (MD) simulations, thus enabling insight into the conformations adopted by, and the dynamics of, the sorbed molecules. The MD

Zbigniew A. Kaszkur; Richard H. Jones; David Waller; R. A. Catlow; John M. Thomas

1993-01-01

300

Image-charge-induced localization of molecular orbitals at metal-molecule interfaces: Self-consistent GW calculations  

NASA Astrophysics Data System (ADS)

Quasiparticle (QP) wave functions, also known as Dyson orbitals, extend the concept of single-particle states to interacting electron systems. Here we employ many-body perturbation theory in the GW approximation to calculate the QP wave functions for a semiempirical model describing a ?-conjugated molecular wire in contact with a metal surface. We find that image charge effects pull the frontier molecular orbitals toward the metal surface, while orbitals with higher or lower energy are pushed away. This affects both the size of the energetic image charge shifts and the coupling of the individual orbitals to the metal substrate. Full diagonalization of the QP equation and, to some extent, self-consistency in the GW self-energy, is important to describe the effect, which is not captured by standard density functional theory or Hartree-Fock. These results should be important for the understanding and theoretical modeling of electron transport across metal-molecule interfaces.

Strange, M.; Thygesen, K. S.

2012-11-01

301

Variationally stable calculations for molecular systems: Polarizabilities and two-photon ionization cross section for the hydrogen molecule  

NASA Astrophysics Data System (ADS)

The variationally stable method of Gao and Starace [B. Gao and A. F. Starace, Phys. Rev. Lett. 61, 404 (1988); Phys. Rev. A 39, 4550 (1989)] has been applied for the first time to the study of multiphoton processes in molecular systems. The generalization in theory is presented, as well as the calculation of properties such as the static and dynamic polarizabilities of the hydrogen molecule and the generalized two-photon ionization cross section. The Schwinger variational iterative method [R. R. Lucchese and V. McKoy, Phys. Rev. A 21, 112 (1980)] has been applied in the achievement of the photoelectron wave function, while a Hartree-Fock representation has been used for the target. This research has been motivated by the scarceness of ab initio calculations of molecular multiphoton ionization cross sections in the literature.

Machado, Andréa M.; Masili, Mauro

2004-04-01

302

Oligogalacturonides: plant damage-associated molecular patterns and regulators of growth and development  

PubMed Central

Oligogalacturonides (OGs) are oligomers of alpha-1,4-linked galacturonosyl residues released from plant cell walls upon partial degradation of homogalacturonan. OGs are able to elicit defense responses, including accumulation of reactive oxygen species and pathogenesis-related proteins, and protect plants against pathogen infections. Recent studies demonstrated that OGs are perceived by wall-associated kinases and share signaling components with microbe-associated molecular patterns. For this reason OGs are now considered true damage-associated molecular patterns that activate the plant innate immunity and may also be involved in the activation of responses to mechanical wounding. Furthermore, OGs appear to modulate developmental processes, likely through their ability to antagonize auxin responses. Here we review our current knowledge on the role and mode of action of this class of oligosaccharides in plant defense and development.

Ferrari, Simone; Savatin, Daniel V.; Sicilia, Francesca; Gramegna, Giovanna; Cervone, Felice; Lorenzo, Giulia De

2013-01-01

303

Single Molecules  

NSDL National Science Digital Library

A new molecular science journal, Single Molecules, from Wiley Interscience, "will provide researchers with a broad overview of current methods and techniques, recent applications and shortcomings of present techniques in the field of single molecules." With temporary free access, the journal's latest issue contains a few full-text articles, with more articles being regularly added. This journal is currently calling for papers.

304

Interstellar molecules  

NASA Astrophysics Data System (ADS)

Complex molecules cycling from circumstellar envelopes through various phases of interstellar matter in the Milky Way are considered. Approximately 65 of the interstellar species detected so far are considered to be organic molecules. By interpreting molecular signatures, it is possible to determine the chemical composition, temperature, mass, internal motions, and evolutionary fate of a dark interstellar cloud.

Verschuur, Gerrit L.

1992-04-01

305

Modeling stochastic kinetics of molecular machines at multiple levels: from molecules to modules.  

PubMed

A molecular machine is either a single macromolecule or a macromolecular complex. In spite of the striking superficial similarities between these natural nanomachines and their man-made macroscopic counterparts, there are crucial differences. Molecular machines in a living cell operate stochastically in an isothermal environment far from thermodynamic equilibrium. In this mini-review we present a catalog of the molecular machines and an inventory of the essential toolbox for theoretically modeling these machines. The tool kits include 1), nonequilibrium statistical-physics techniques for modeling machines and machine-driven processes; and 2), statistical-inference methods for reverse engineering a functional machine from the empirical data. The cell is often likened to a microfactory in which the machineries are organized in modular fashion; each module consists of strongly coupled multiple machines, but different modules interact weakly with each other. This microfactory has its own automated supply chain and delivery system. Buoyed by the success achieved in modeling individual molecular machines, we advocate integration of these models in the near future to develop models of functional modules. A system-level description of the cell from the perspective of molecular machinery (the mechanome) is likely to emerge from further integrations that we envisage here. PMID:23746505

Chowdhury, Debashish

2013-06-01

306

Pattern-based sensing of peptides and aminoglycosides with a single molecular probe.  

PubMed

A coumarin-based molecular probe can be used for the sensing of peptides and aminoglycoside antibiotics. The probe reacts with the primary amine group(s) of the analytes to give a mixture of covalent adducts with distinct colors. Each analyte gives rise to a characteristic UV-vis spectrum. A pattern-based analysis of the spectra allows identifying structurally related analytes. Furthermore, it is possible to obtain information about the quantity and the purity of the analytes. PMID:23796050

Lee, Boram; Chen, Shiyu; Heinis, Christian; Scopelliti, Rosario; Severin, Kay

2013-06-24

307

The stability of the 2D Penrose pattern: molecular dynamics study  

Microsoft Academic Search

The stability of the 2D Penrose pattern was studied by the molecular dynamics method. The potential used here is the Lennard-Jones type, the parameters of which were determined to stabilise the FCC(111) structure. All the systems studied are unstable and decompose into the FCC(111) structure; the system of 76 atoms changed into the single crystal, namely the FCC(111), and the

Y. Sasajima; T. Miura; M. Ichimura; M. Imabayashi; R. Yamamoto

1987-01-01

308

ATOMIC AND MOLECULAR PHYSICS: A Time-Dependent Wavepacket Method for Photodissociation Dynamics of Triatomic Molecule  

NASA Astrophysics Data System (ADS)

We report a time-dependent quantum wavepacket theory employed to interpret the photoabsorption spectrum of the N2O molecule in terms of the nuclear motion on the upper 21A? and 11A? potential energy surfaces. The N2-O bond breaks upon excitation leading to dissociation. The total angular momentum is treated correctly taking into account the vector property of the electric field of the exciting radiation.

Mohammad Noh, Daud; Gabriel, Balint-Kurti G.

2009-07-01

309

Molecular regulation of intercellular adhesion molecule 1 (ICAM-1) expression in renal cell carcinoma  

Microsoft Academic Search

Intercellular adhesion molecule-1 (ICAM-1) mediates two important functional. aspects of tumor biology, namely enhancement of tumor metastasis and mediation of host defense mechanisms such as lymphocyte-mediated tumor cytotoxicity. Since ICAM-1 is expressed by most renal cell carcinomas (RCC), the regulation of ICAM-1 expression is important in understanding the biological behavior of RCC. We report an investigation on ICAM-1 expression and

K. Tanabe; S. C. Campbell; J. P. Alexander; F. Steinbach; M. G. Edinger; R. R. Tubbs; A. C. Novick; E. A. Klein

1997-01-01

310

Molecular Dynamics Simulation of Dextran Extension by Constant Force in Single Molecule AFM  

Microsoft Academic Search

The extension of 1–6 polysaccharides has been studied in a series of recent single molecule AFM experiments. For dextran, a key finding was the existence of a plateau in the force-extension curve at forces between 700 and 1000pN. We studied the extension of the dextran 10-mer under constant force using atomistic simulation with various force fields. All the force fields

Igor M. Neelov; David B. Adolf; Tom C. B. McLeish; Emanuele Paci

2006-01-01

311

Molecular Mechanics of Single Protein Molecules Measured with the Atomic Force Microscope  

NASA Astrophysics Data System (ADS)

After a short history of AFM development in our lab, including recent developments with small cantilevers, this talk will focus on 1) pulling single protein molecules to explore the forces involved in unfolding and 2) watching single protein molecules in action to learn how they function mechanically. 1) Pulling experiments on proteins used as marine adhesives in abalone shells and other biological composite materials reveal modules bound together by sacrificial bonds that are weaker than the backbone bonds in the polypeptide chain.1 These self-healing modules provide effective energy absorption and appear to be a real key to understanding the impressive fracture resistance of biological composite materials. For example, the abalone shell is 3000 times more fracture resistant than a single crystal of calcium carbonate, despite the fact that 97% of the mass of the shell is crystalline calcium carbonate. 2) It is becoming possible, again with AFMs, to learn how some enzymes, nature's nanomachines, do their exquisite materials synthesis and processing. The talk will focus on the chaperonin system of GroEL and GroES that processes incorrectly folded proteins and assists them in refolding correctly. It is becoming possible not only to see single molecule events such as the association and disassociation of the GroEL-Gro-ES complex, but also to measure potential energy functions for the molecules in various conformational states. These new measurements, together with detailed structural measurements from other techniques, give new clues about how these proteins use the energy of ATP to do their work. Since the AFMs of today are very far from fundamental limits, this is only the beginning. 1. B. L. Smith, T. E. Schaffer, M. Viani, J. B. Thompson, N. A. Frederick, J. Kindt, A. Belcher, G. D. Stucky, D. E. Morse and P. K. Hansma, Nature 399, 761 (1999)

Hansma, Paul K.

2000-03-01

312

The signature molecular descriptor. 4. Canonizing molecules using extended valence sequences.  

PubMed

We present a new algorithm to canonize molecular graphs using the signature molecular descriptor introduced in the previous papers of this series. While developed specifically for molecular structures, the algorithm can be used for any graph and is not limited to acyclic graphs, planar graphs, bounded valence, or bounded genus graphs, for which polynomial time algorithms exist. The algorithm is tested with benzenoid hydrocarbons and a database of 126,705 organic compounds. The algorithm's performances are compared against Brendan Mc Kay's Nauty algorithm, which is believed to be the fastest graph canonization algorithm for general graphs, with five series of graphs each comprising up to 30,000 vertices: 2D meshes (pericondensed benzenoids), 3D cages (fullerenes and nanotubes), 3D meshes (crystal lattices), 4D cages, and power law graphs (protein and gene networks). The algorithm can be downloaded as an open source code at http://www.cs.sandia.gov/ approximately jfaulon/QSAR. PMID:15032522

Faulon, Jean-Loup; Collins, Michael J; Carr, Robert D

313

Multicomponent redox catalysts for reduction of large biological molecules using molecular hydrogen as the reductant  

SciTech Connect

One-electron reduction of the large biological molecules horse heart cytochrome c, sperm whale myoglobin, and horseradish peroxidase using H/sub 2/ as the reductant can be catalyzed by two-component, high surface area heterogeneous catalysts. The catalysts can be prepared by first functionalizing high surface area SiO/sub 2/ with a polycationic polymer into which is dispersed MCl/sub 4//sup 2 -/ (M = Pd, Pt). Reduction with H/sub 2/ yields elemental Pd or Pt dispersed in the polymer. The particles are finally functionalized with a redox polymer derived from hydrolysis of Si(OR)/sub 3/ groups of an N,N'-dialkyl-4,4'-bipyridinium- or from a cobalticenium-based monomer. The two components of the heterogeneous catalysts are the buried noble metal capable of activating the H/sub 2/ and the redox polymer, which can equilibrate both with the noble metal and with the large biological molecule. Reduction of the large biological molecules in aqueous solution can be effected at room temperature and 1 atm H/sub 2/ using the catalysts under conditions where the biological materials would not be reducible with H/sub 2/ alone or when the noble metal alone would be used as the catalyst.

Chao, S.; Simon, R.A.; Mallouk, T.E.; Wrighton, M.S.

1988-03-30

314

Resonance enhanced multiphoton and single-photon ionization of molecules and molecular fragments. Final report, May 1993--April 1997  

SciTech Connect

Resonance enhanced multiphoton ionization (REMPI) utilizes pulsed laser radiation to prepare a molecule in an excited state via absorption of one or more photons and to subsequently ionize that level before it decays. A remarkable feature of REMPI is that the very narrow bandwidth of laser radiation makes it possible to select a specific rotational level in the initial (ground) state and to prepare the excited state of interest in a single rotational level. Thus, by suitable choice of the excitation step, it is possible to selectively ionize a species that may be present. The key objective of the effort is to carry out quantitative studies of REMPI of molecules and molecular fragments, as well as of single-photon ionization of these species by coherent VUV radiation, in order to provide a robust description of significant spectral features of interest in related experiments and needed insight into the underlying dynamics of these spectra. A major focus of the effort is joint theoretical and experimental studies of these ion rotational distributions which are being widely studied by the zero-kinetic-energy (ZEKE) technique. This technique, which is based on the detection of photoelectrons resulting from pulsed-field ionization of very high Rydberg states lying just below an ion threshold, makes it possible to obtain cation distributions with subwavenumber resolution. The unprecedented resolution of this ZEKE technique is opening up entirely new vistas in studies of photoionization dynamics, ion spectroscopy, and state-selected ion-molecule reactions. Emerging applications built on the ultra-high resolution of this technique include its use for accurate determination of thermochemically important ionization energies, for characterization of ion rovibrational level structure of large organic molecules, of elemental clusters, and of weakly bound molecular complexes, for probing reactive fragments, and for pump-probe photoelectron studies of wavepacket dynamics. This surge of experimental activity in ultra-high resolution studies of molecular photoelectron spectra continues to raise new theoretical challenges and has provided the stimulus for several of the collaborations with experimental groups in North America and Europe.

McKoy, V.

1998-09-01

315

Meet the Molecules in Chocolate: Informal Opportunities for Building Thematic Molecular Models with Children  

ERIC Educational Resources Information Center

|We describe the development and use of a molecular model building activity with a chocolate theme, suitable for a public presentation of chemistry through interaction with visitors to science festivals and museums, and as a special classroom activity during science weeks, and so forth. (Contains 3 figures.)|

Amey, Jennifer R.; Fletcher, Matthew D.; Fletcher, Rachael V.; Jones, Alison; Roberts, Erica W.; Roberts, Ieuan O.

2008-01-01

316

Activity Coefficients of Complex Molecules by Molecular Simulation and Gibbs-Duhem Integration  

Microsoft Academic Search

Activity coefficients of solvents and solutes in different aqueous solutions of alcohols and polymers are determined by molecular dynamic simulations. These data are often not accessible by simulation due to unacceptably high computational demands. Therefore, we applied a combination of two methods: water activity coefficients were determined directly via Overlapping Distribution Method, while counter-component activity coefficients were calculated indirectly by

Sascha Hempel; Jan Fischer; Dietmar Paschek; Gabriele Sadowski

2012-01-01

317

Relationship between Molecular Structure, Concentration and Odor Qualities of Oxygenated Aliphatic Molecules  

Microsoft Academic Search

Increasing the concentration of an odorant increases the number of receptor cells and glomeruli in the olfactory bulb that are stimulated, and it is commonly acknowledged that these represent increased numbers of receptor types. Currently, it is not known whether a receptor type is associated with a unique quality and a unique molecular feature of an odorant, or its activation

D. G. Laing; P. K. Legha; A. L. Jinks; I. Hutchinson

2003-01-01

318

Friction and energy dissipation mechanisms in adsorbed molecules and molecularly thin films  

Microsoft Academic Search

This review provides an overview of recent advances that have been achieved in understanding the basic physics of friction and energy dissipation in molecularly thin adsorbed films and the associated impact on friction at microscopic and macroscopic length scales. Topics covered include a historical overview of the fundamental understanding of macroscopic friction, theoretical treatments of phononic and electronic energy dissipation

Jacqueline Krim

2012-01-01

319

Meet the Molecules in Chocolate: Informal Opportunities for Building Thematic Molecular Models with Children  

ERIC Educational Resources Information Center

We describe the development and use of a molecular model building activity with a chocolate theme, suitable for a public presentation of chemistry through interaction with visitors to science festivals and museums, and as a special classroom activity during science weeks, and so forth. (Contains 3 figures.)

Amey, Jennifer R.; Fletcher, Matthew D.; Fletcher, Rachael V.; Jones, Alison; Roberts, Erica W.; Roberts, Ieuan O.

2008-01-01

320

Matrix and substrate effects on the sputtering of a 2 kDa molecule: Insights from molecular dynamics  

NASA Astrophysics Data System (ADS)

In an effort towards a more accurate theoretical description of matrix and substrate effects in organic sputtering, we report on molecular dynamics simulations of the desorption induced by 500 eV Ar projectiles bombarding samples composed of polystyrene (PS) oligomers embedded in a trimethylbenzene matrix or cast on a silver substrate. The ejection of intact PS molecules, sometimes accompanied by matrix molecules/silver atoms, is observed in the first 10 ps following the impact. For the ``matrix'' sample, the results indicate that the emission of large amounts of organic material is mostly vibrationally induced. Extended calculations show that matrix:analyte clusters decay after emission, liberating the analyte in flight. In the case of the ``substrate'' sample, the emission is oftentimes the result of the concerted upward motion of several metal atoms underneath the molecule. Finally, the comparison between a matrix:analyte sample confined in a nanostructured silver crystal and a purely organic sample under identical bombardment conditions shows that the presence of the silver medium significantly enhances the desorption yields.

Delcorte, A.; Arezki, B.; Garrison, B. J.

2003-12-01

321

Dissociation of molecular iodine in a flow tube in the presence of O2(1?) molecules.  

PubMed

Molecular iodine dissociates in the presence of O(2)((1)?) and O(2)((1)?) molecules, but the mechanism of this process is not completely understood. In this paper, using flow tube experiments, we studied the initiation stage of iodine dissociation. Absolute spectral irradiance measurements were employed for measurements of concentrations of electronically excited particles. It was found that under the present experimental conditions initiation of iodine dissociation is mainly caused by reaction O(2)((1)?) + I(2) ? O(2)((3)?) + 2I with a rate constant of (9.3 ± 2.0) × 10(-11) cm(3) s(-1). An appreciable role of the O(2)((1)?) molecule as the dissociation initiator has not been observed. It was observed that the growth rate of iodine atoms sharply accelerated when the concentration of I((2)P(1/2)) atoms approached 2 × 10(-4) of O(2)((1)?) concentration or when production rates of O(2)((1)?) molecules in reactions O(2)((1)?) + I((2)P(1/2)) and O(2)((1)?) + O(2)((1)?) became equal. PMID:23009345

Zagidullin, Marsel V; Khvatov, Nickolay A; Malyshev, Michael S; Svistun, Michael I

2012-10-05

322

Interaction between Water Molecules and Zinc Sulfide Nanoparticles Studied by Temperature-Programmed Desorption and Molecular Dynamics Simulations.  

SciTech Connect

The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. We have investigated the bonding of water molecules to the surfaces of ZnS nanoparticles (2-3 nm sphalerite) using temperature-programmed desorption (TPD). The activation energy for water desorption was derived as a function of the surface coverage through kinetic modeling of the experimental TPD curves. The binding energy of water equals the activation energy of desorption if it is assumed that the activation energy for adsorption is nearly zero. Molecular dynamics (MD) simulations of water adsorption on 3 and 5 nm sphalerite nanoparticles provided insights into the adsorption process and water binding at the atomic level. Water binds with the ZnS nanoparticle surface mainly via formation of Zn-O bonds. As compared with bulk ZnS crystals, ZnS nanoparticles can adsorb more water molecules per unit surface area due to the greatly increased curvature, which increases the distance between adjacent adsorbed molecules. Results from both TPD and MD show that the water binding energy increases with decreasing the water surface coverage. We attribute the increase in binding energy with decreasing surface water coverage to the increasing degree of surface under-coordination as removal of water molecules proceeds. MD also suggests that the water binding energy increases with decreasing particle size due to the further distance and hence lower interaction between adsorbed water molecules on highly curved smaller particle surfaces. Results also show that the binding energy, and thus the strength of interaction of water, is highest in isolated nanoparticles, lower in nanoparticle aggregates, and lowest in bulk crystals. Given that water binding is driven by surface energy reduction, we attribute the decreased binding energy for aggregated as compared to isolated particles to the decrease in surface energy that occurs as the result of inter-particle interactions.

Zhang, Hengzon; Rustad, James R.; Banfield, Jillian F.

2007-05-23

323

Initiating molecular growth in the interstellar medium via dimeric complexes of observed ions and molecules  

NASA Astrophysics Data System (ADS)

A feasible initiation step for particle growth in the interstellar medium (ISM) is simulated by means of ab initio quantum chemistry methods. The systems studied are dimer ions formed by pairing nitrogen containing small molecules known to exist in the ISM with ions of unsaturated hydrocarbons or vice versa. Complexation energies, structures of ensuing complexes and electronic excitation spectra of the encounter complexes are estimated using various quantum chemistry methods. Møller-Plesset perturbation theory (MP2), Z-averaged perturbation theory (ZAPT2), coupled cluster singles and doubles with perturbative triples corrections (CCSD(T)), and density functional theory (DFT) methods (B3LYP) were employed along with the correlation consistent cc-pVTZ and aug-cc-pVTZ basis sets. Two types of complexes are predicted. One type of complex has electrostatic binding with moderate (7-20 kcal mol-1) binding energies, that are nonetheless significantly stronger than typical van der Waals interactions between molecules of this size. The other type of complex develops strong covalent bonds between the fragments. Cyclic isomers of the nitrogen containing complexes are produced very easily by ion-molecule reactions. Some of these complexes show intense ultraviolet-visible spectra for electronic transitions with large oscillator strengths at the B3LYP, ?B97, and equations of motion coupled cluster (EOM-CCSD) levels. The open shell nitrogen containing carbonaceous complexes especially exhibit a large oscillator strength electronic transition in the visible region of the electromagnetic spectrum. Appendix A is available in electronic form at http://www.aanda.org

Bera, Partha P.; Head-Gordon, Martin; Lee, Timothy J.

2011-11-01

324

Nonequilibrium molecular dynamics of the rheological and structural properties of linear and branched molecules. Simple shear and poiseuille flows; instabilities and slip  

NASA Astrophysics Data System (ADS)

Nonequilibrium molecular-dynamics simulations are performed for linear and branched chain molecules to study their rheological and structural properties under simple shear and Poiseuille flows. Molecules are described by a spring-monomer model with a given intermolecular potential. The equations of motion are solved for shear and Poiseuille flows with Lees and Edward's [A. W. Lees and S. F. Edwards, J. Phys. C 5, 1921 (1972)] periodic boundary conditions. A multiple time-scale algorithm extended to nonequilibrium situations is used as the integration method, and the simulations are performed at constant temperature using Nosé-Hoover [S. Nosé, J. Chem. Phys. 81, 511 (1984)] dynamics. In simple shear, molecules with flow-induced ellipsoidal shape, having significant segment concentrations along the gradient and neutral directions, exhibit substantial flow resistance. Linear molecules have larger zero-shear-rate viscosity than that of branched molecules, however, this behavior reverses as the shear rate is increased. The relaxation time of the molecules is associated with segment concentrations directed along the gradient and neutral directions, and hence it depends on structure and molecular weight. The results of this study are in qualitative agreement with other simulation studies and with experimental data. The pressure (Poiseuille) flow is induced by an external force Fe simulated by confining the molecules in the region between surfaces which have attractive forces. Conditions at the boundary strongly influence the type of the slip flow predicted. A parabolic velocity profile with apparent slip on the wall is predicted under weakly attractive wall conditions, independent of molecular structure. In the case of strongly attractive walls, a layer of adhered molecules to the wall produces an abrupt distortion of the velocity profile which leads to slip between fluid layers with magnitude that depends on the molecular structure. Finally, the molecular deformation under flow depends on the attractive force of the wall, in such a way that molecules are highly deformed in the case of strong attracting walls.

Castillo-Tejas, Jorge; Alvarado, Juan F. J.; González-Alatorre, Guillermo; Luna-Bárcenas, Gabriel; Sanchez, Isaac C.; Macias-Salinas, Ricardo; Manero, Octavio

2005-08-01

325

Nonequilibrium molecular dynamics of the rheological and structural properties of linear and branched molecules. Simple shear and poiseuille flows; instabilities and slip.  

PubMed

Nonequilibrium molecular-dynamics simulations are performed for linear and branched chain molecules to study their rheological and structural properties under simple shear and Poiseuille flows. Molecules are described by a spring-monomer model with a given intermolecular potential. The equations of motion are solved for shear and Poiseuille flows with Lees and Edward's [A. W. Lees and S. F. Edwards, J. Phys. C 5, 1921 (1972)] periodic boundary conditions. A multiple time-scale algorithm extended to nonequilibrium situations is used as the integration method, and the simulations are performed at constant temperature using Nose-Hoover [S. Nose, J. Chem. Phys. 81, 511 (1984)] dynamics. In simple shear, molecules with flow-induced ellipsoidal shape, having significant segment concentrations along the gradient and neutral directions, exhibit substantial flow resistance. Linear molecules have larger zero-shear-rate viscosity than that of branched molecules, however, this behavior reverses as the shear rate is increased. The relaxation time of the molecules is associated with segment concentrations directed along the gradient and neutral directions, and hence it depends on structure and molecular weight. The results of this study are in qualitative agreement with other simulation studies and with experimental data. The pressure (Poiseuille) flow is induced by an external force F(e) simulated by confining the molecules in the region between surfaces which have attractive forces. Conditions at the boundary strongly influence the type of the slip flow predicted. A parabolic velocity profile with apparent slip on the wall is predicted under weakly attractive wall conditions, independent of molecular structure. In the case of strongly attractive walls, a layer of adhered molecules to the wall produces an abrupt distortion of the velocity profile which leads to slip between fluid layers with magnitude that depends on the molecular structure. Finally, the molecular deformation under flow depends on the attractive force of the wall, in such a way that molecules are highly deformed in the case of strong attracting walls. PMID:16108693

Castillo-Tejas, Jorge; Alvarado, Juan F J; González-Alatorre, Guillermo; Luna-Bárcenas, Gabriel; Sanchez, Isaac C; Macias-Salinas, Ricardo; Manero, Octavio

2005-08-01

326

Universal scaling behavior of molecular electronic stopping cross section for protons colliding with small molecules and nucleobases  

NASA Astrophysics Data System (ADS)

The electronic stopping cross section and mean excitation energy for molecules and 5 nucleobases have been calculated within the first Born approximation in terms of an orbital decomposition to take into account the molecular structure. The harmonic oscillator (HO) description of the stopping cross section together with a Floating Spherical Gaussian Orbital (FSGO) model is implemented to account for the chemical composition of the target. This approach allows us to use bonds, cores, and lone pairs as HO basis to describe the ground state molecular structure. In the HO model, the orbital angular frequency is the only parameter that connects naturally with the mean excitation energy. As a result, we obtain a simple expression for the equivalent mean excitation energy in terms of the orbital radius parameter, as well as an analytical expression of the stopping cross section. For gas phase molecular targets, we provide HO based orbital mean excitation energies to describe any molecule containing C, N, O, H, and P atoms. We present results for protons colliding with H2, N2, O2, H2O, CO2, propylene (C3H6), methane (CH4), ethylene (C2H4) and the nucleobases - guanine (C5H5N5O), cytosine (C4H5N2O2), thymine (C5H6N2O2), adenine (C5H5N5) and uracil (C4H4N2O2). The results for the stopping cross section are compared with available experimental and theoretical data showing good to excellent agreement in the region of validity of the model. The HO approach allows us to obtain a universal stopping cross section formula to describe a universal scaling behavior for the energy loss process. The universal scaled curve is confirmed by the experimental data.

Trujillo-López, L. N.; Martínez-Flores, C.; Cabrera-Trujillo, R.

2013-10-01

327

Single ionization of hydrogen molecules by fast protons as a function of the molecular alignment  

SciTech Connect

Relative cross sections for the 4 MeV H{sup +}+D{sub 2} ({sup 1}{sigma}{sub g}{sup +}){yields}H{sup +}+D{sub 2}{sup +}(1s{sigma})+e{sup -} ionization process were measured as a function of the molecular alignment during the interaction. The angle between the molecular axis and the projectile was obtained by using a momentum imagining technique and isolating the events in which the D{sub 2}{sup +}(1s{sigma}) ions are excited to the vibrational continuum and subsequently dissociate. While anisotropic cross sections have been observed in the past for a number of collision processes involving both target electrons, the one electron process investigated here is isotropic within our experimental uncertainties.

Johnson, Nora G. [Department of Physics, Augustana College, Sioux Falls, South Dakota 57197 (United States); J.R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhattan, Kansas 66506 (United States); Mello, R. N.; Lundy, Michael E.; Kapplinger, J.; Wells, E. [Department of Physics, Augustana College, Sioux Falls, South Dakota 57197 (United States); Parke, Eli; Carnes, K. D.; Ben-Itzhak, I. [J.R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhattan, Kansas 66506 (United States)

2005-11-15

328

Molecular complexes of antipsychotic pharmaceutical parent molecule phenothiazine and unsaturated acid anhydrides  

NASA Astrophysics Data System (ADS)

The charge-transfer complexes (CTC) between a parent molecule of antipsychotic pharmaceuticals, phenothiazine, and seven unsaturated acid anhydrides, 1,4,5,8-naphtalenetetracarboxylic dianhydride, diphenic anhydride, maleic anhydride (MA), 3,4,5,6-tetrahydrophthalic anhydride (THPA), 3-hydroxy-1,8-naphthalic anhydride (HONA), 4-chloro-1,8-naphthalic anhydride (ClNA), and 1,8-naphthalic anhydride (NA) were studied using IR and UV spectroscopy. Stability constants ( K) at different temperatures were measured, and based on the K's ? H and ? S were calculated. The values of electron affinity ( EA) of anhydrides were obtained according to Mulliken's theory. The results show that phenothiazine is an excellent donor and has strong ability to complex with the carbonyl group, and the EA values have good linear relationships with ? H and K, respectively. The solvent effect on CTCs was also determined and explained. The CTC of phenothiazine-succinic anhydride (SA) was studied under the same conditions. It was deduced from the results obtained that there were two charge-accepting centers in the unsaturated acid anhydrides when they formed CTCs with phenothiazine. The first one was carbon atom of the two carbonyl groups and the second one was their ?C?C? in the molecules.

Song, Hua-Can; Huan, Ping; Ying, Bai-Ning

2003-05-01

329

Lipid molecules induce p38? activation via a novel molecular switch.  

PubMed

p38? mitogen-activated protein kinase (MAPK) is generally activated by dual phosphorylation but has also been shown to exhibit alternative activation modes. One of these modes included a direct interaction with phosphatidylinositol ether lipid analogues (PIA) inducing p38? autoactivation and apoptosis. Perifosine, an Akt inhibitor in phase II clinical trials, also showed p38? activation properties similarly to those of PIAs. The crystal structures of p38? in complex with PIA23, PIA24 and perifosine provide insights into this unique activation mode. The activating molecules bind a unique hydrophobic binding site in the kinase C'-lobe formed in part by the MAPK insert region. In addition, there are conformational changes in the short ?EF/?F loop region that acts as an activation switch, inducing autophosphorylation. Structural and biochemical characterization of the ?EF/?F loop identified Trp197 as a key residue in the lipid binding and in p38? catalytic activity. The lipid binding site also accommodates hydrophobic inhibitor molecules and, thus, can serve as a novel p38?-target for specific activation or inhibition, with novel therapeutic implications. PMID:23079240

Tzarum, Netanel; Eisenberg-Domovich, Yael; Gills, Joell J; Dennis, Phillip A; Livnah, Oded

2012-10-16

330

Measuring polarizability anisotropies of rare gas diatomic molecules by laser-induced molecular alignment technique.  

PubMed

The polarizability anisotropies of homonuclear rare gas diatomic molecules, Ar(2), Kr(2), and Xe(2), are investigated by utilizing the interaction of the induced electric dipole moment with a nonresonant, nanosecond laser pulse. The degree of alignment, which depends on the depth of the interaction potential created by the intense laser field, is measured, and is found to increase in order of Ar(2), Kr(2), and Xe(2) at the same peak intensity. Compared with a reference I(2) molecule, Ar(2), Kr(2), and Xe(2) are found to have the polarizability anisotropies of 0.45 ± 0.13, 0.72 ± 0.13, and 1.23 ± 0.21 A?(3), respectively, where the uncertainties (one standard deviation) in the polarizability anisotropies are carefully evaluated on the basis of the laser intensity dependence of the degree of alignment. The obtained values are compared with recent theoretical calculations and are found to agree well within the experimental uncertainties. PMID:21663360

Minemoto, Shinichirou; Sakai, Hirofumi

2011-06-01

331

Dissociative electron attachment to unstable molecules and slow fragmentation of metastable molecular anions  

NASA Astrophysics Data System (ADS)

Recent experimental investigations of dissociative electron attachment to unstable molecules and free radicals are reviewed along with observations of metastable negatively charged ions. Measurements have been made with a time-of-flight mass spectrometer in Belfast and also, for metastable ions, with a double focussing twin field mass spectrometer in Innsbruck. Electron attachment to unstable CS, for example, was found to be similar to electron attachment to the valence isoelectronic CO molecule with observation of S- and C- ions just above the thermodynamic threshold for S- + C (3P) at 5.43 eV, C-+ S at 6.40 eV and S-+ C(1D) at 6.70 eV with peak cross sections of ~ 0.025 Å2, 0.002 Å2 and 0.003 Å2 respectively. Slow fragmentation of metastable SF-*6 formed in low energy electron attachment to SF6 has been observed on microsecond timescales in competition with autodetachment; processes SF-*6 ? SF-5 + F and SF-*6 ? SF6 + e- respectively. Fragmentation of metastable anions of benzene derivatives, such as 2,4-dinitro-toluene [CH3.C6H3(NO2)2], has also been observed on microsecond timescales.

Field, T. A.; Graupner, K.; Mauracher, A.; Scheier, P.; Bacher, A.; Denifl, S.; Zappa, F.; Märk, T. D.

2007-11-01

332

Effect of molecular structure on fragmentation of isolated organic molecules in solid rare gas matrices  

NASA Astrophysics Data System (ADS)

The effect of excess energy on the primary radical cations of bifunctional carbonyl compounds and aliphatic alkynes was simulated by matrix isolation method using rare gas matrices with various ionization potentials. The formation of fragmentation products was monitored by EPR and FTIR spectroscopy. It was shown that the radical cations of bifunctional compounds (CH3OCH2COCH3 and CH3COCOCH3) dissociated effectively yielding CH3 radicals upon irradiation in solid argon matrix at T?16 K. In addition to isolated methyl radicals, the radical pairs consisting of two methyl radicals separated by two CO molecules were detected in the case of diacetyl. The probability of fragmentation decreases with the decreasing excess energy by switching from Ar to Xe. In general, bifunctional molecules were found to be less stable to “hot” ionic fragmentation in low-temperature solids in comparison with simple prototype compounds. In the case of alkynes of the R?C?CH type, a noticeable yield of fragmentation products was observed when R=-C(CH3)3, but it was negligible for R=-CH3. The mechanisms of “hot” reactions and excess energy relaxation are discussed.

Kobzarenko, A. V.; Sukhov, F. F.; Orlov, A. Yu.; Kovalev, G. V.; Baranova, I. A.; Feldman, V. I.

2012-09-01

333

Dehydrogenation of gaseous hydrogen-containing molecules: The formation of elemental and molecular clusters  

SciTech Connect

A general concept employing the dehydrogenation of hydrogen-containing organic and inorganic compounds is shown to readily affect the production of a wide variety of elemental and binary clusters. Hydrogen-containing molecules such as C[sub 2]H[sub 4], NH[sub 3], SiH[sub 4], H[sub 2]S, or H[sub 2]O, are introduced into an extremely energetic plasma generated from laser irradiation of a metal surface; this plasma dehydrogenates the molecules to produce nascent C, N, Si, S, and O atoms. These C, N, Si, S, and O atoms can react with metal atoms or ions contained in the plasma and form metallocarbohedrenes or metal-carbide, metal-nitride, metal-silicide, metal-sulfide, or metal-oxide clusters. Alternatively, individual constituents may associate to produce pure elemental clusters such as those comprised of carbon or silicon. In principle, this technique can be applied to all gaseous hydrogen-containing compounds. The results of the present study provide an alternative way (in some cases it could be the only feasible way) to generate clusters of these materials. Study of the ensuing distributions provides unique insight into the cluster-formation mechanisms involving this type of cluster source.

Chen, Z.Y.; Walder, G.J.; Castleman, A.W. Jr. (Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802 (United States))

1994-01-15

334

Molecular understanding of atmospheric particle formation from sulfuric acid and large oxidized organic molecules.  

PubMed

Atmospheric aerosols formed by nucleation of vapors affect radiative forcing and therefore climate. However, the underlying mechanisms of nucleation remain unclear, particularly the involvement of organic compounds. Here, we present high-resolution mass spectra of ion clusters observed during new particle formation experiments performed at the Cosmics Leaving Outdoor Droplets chamber at the European Organization for Nuclear Research. The experiments involved sulfuric acid vapor and different stabilizing species, including ammonia and dimethylamine, as well as oxidation products of pinanediol, a surrogate for organic vapors formed from monoterpenes. A striking resemblance is revealed between the mass spectra from the chamber experiments with oxidized organics and ambient data obtained during new particle formation events at the Hyytiälä boreal forest research station. We observe that large oxidized organic compounds, arising from the oxidation of monoterpenes, cluster directly with single sulfuric acid molecules and then form growing clusters of one to three sulfuric acid molecules plus one to four oxidized organics. Most of these organic compounds retain 10 carbon atoms, and some of them are remarkably highly oxidized (oxygen-to-carbon ratios up to 1.2). The average degree of oxygenation of the organic compounds decreases while the clusters are growing. Our measurements therefore connect oxidized organics directly, and in detail, with the very first steps of new particle formation and their growth between 1 and 2 nm in a controlled environment. Thus, they confirm that oxidized organics are involved in both the formation and growth of particles under ambient conditions. PMID:24101502

Schobesberger, Siegfried; Junninen, Heikki; Bianchi, Federico; Lönn, Gustaf; Ehn, Mikael; Lehtipalo, Katrianne; Dommen, Josef; Ehrhart, Sebastian; Ortega, Ismael K; Franchin, Alessandro; Nieminen, Tuomo; Riccobono, Francesco; Hutterli, Manuel; Duplissy, Jonathan; Almeida, João; Amorim, Antonio; Breitenlechner, Martin; Downard, Andrew J; Dunne, Eimear M; Flagan, Richard C; Kajos, Maija; Keskinen, Helmi; Kirkby, Jasper; Kupc, Agnieszka; Kürten, Andreas; Kurtén, Theo; Laaksonen, Ari; Mathot, Serge; Onnela, Antti; Praplan, Arnaud P; Rondo, Linda; Santos, Filipe D; Schallhart, Simon; Schnitzhofer, Ralf; Sipilä, Mikko; Tomé, António; Tsagkogeorgas, Georgios; Vehkamäki, Hanna; Wimmer, Daniela; Baltensperger, Urs; Carslaw, Kenneth S; Curtius, Joachim; Hansel, Armin; Petäjä, Tuukka; Kulmala, Markku; Donahue, Neil M; Worsnop, Douglas R

2013-10-07

335

Determination of molecular formulas of natural organic matter molecules by (ultra-) high-resolution mass spectrometry  

Microsoft Academic Search

Electrospray ionization (ESI) combined with ultra-high-resolution mass spectrometry on a Fourier transform ion cyclotron resonance mass spectrometer has been shown to be a very powerful tool for the analysis of fulvic and humic acids and of natural organic matter (NOM) at the molecular level. With this technique thousands of ions can be separated from each other and their m\\/z ratio

Thorsten Reemtsma

2009-01-01

336

Identification of DNA adduct formation of small molecules by molecular descriptors and machine learning methods  

Microsoft Academic Search

In this study, we developed new computational DNA adduct prediction models by using significantly more diverse training data-set of 217 DNA adducts and 1024 non-DNA adducts, and applying five machine learning methods which include support vector machine (SVM), k-nearest neighbour, artificial neural networks, logistic regression and continuous kernel discrimination. The molecular descriptors used for DNA adduct prediction were selected from

Hanbing Rao; Xianyin Zeng; Yanying Wang; Hua He; Feng Zhu; Zerong Li; Yuzong Chen

2012-01-01

337

Identification of DNA adduct formation of small molecules by molecular descriptors and machine learning methods  

Microsoft Academic Search

In this study, we developed new computational DNA adduct prediction models by using significantly more diverse training data-set of 217 DNA adducts and 1024 non-DNA adducts, and applying five machine learning methods which include support vector machine (SVM), k-nearest neighbour, artificial neural networks, logistic regression and continuous kernel discrimination. The molecular descriptors used for DNA adduct prediction were selected from

Hanbing Rao; Xianyin Zeng; Yanying Wang; Hua He; Feng Zhu; Zerong Li; Yuzong Chen

2011-01-01

338

Quantitative surface analysis of molecular overlayers by resonantly enhanced multiphoton ionization of sputtered molecules  

NASA Astrophysics Data System (ADS)

Laser postionization of sputtered neutrals in combination with resonantly enhanced multiphoton ionization is a more quantitative analytical technique for organic surface analysis than secondary ion mass spectrometry due to the reduced matrix effect. Nevertheless, we observed a remaining sputter-induced matrix effect. We have investigated this matrix effect by comparing the secondary neutral and ion emissions from UHV-deposited molecular overlayers of adenine and ?-alanine on Ag substrates under Ar+, Xe+, and SF5+ primary ion bombardment. .

Schnieders, A.; Rüschenschmidt, K.; Schröder, M.; Benninghoven, A.; Arlinghaus, H. F.

2001-08-01

339

Small molecule penetrant diffusion in aromatic polyesters: a molecular dynamics simulation study  

Microsoft Academic Search

Molecular dynamics (MD) simulations have been used to study diffusion of methane in three highly impermeable aromatic polyesters that are good barrier materials. These are amorphous poly(ethylene terephthalate) (PET) and poly(ethylene 2,6-naphthalene dicarboxylate) (PEN), and the nematic mesophase of the thermotropic liquid crystalline copolyester (LCP) of p-hydroxy benzoic acid (HBA) and 2,6 hydroxy naphthoic acid (HNA). Diffusion coefficients were determined

Rishikesh K. Bharadwaj; Richard H. Boyd

1999-01-01

340

Molecular imaging of cell death in vivo by a novel small molecule probe  

Microsoft Academic Search

Apoptosis has a role in many medical disorders, therefore assessment of apoptosis in vivo can be highly useful for diagnosis, follow-up and evaluation of treatment efficacy. ApoSense is a novel technology, comprising low molecular-weight probes, specifically designed for imaging of cell death in vivo. In the current study we present targeting and imaging of cell death both in vitro and

Revital Aloya; Anat Shirvan; Hagit Grimberg; Ayelet Reshef; Galit Levin; Dvora Kidron; Avi Cohen; Ilan Ziv

2006-01-01

341

Molecular patterns of X chromosome-linked color vision genes among 134 menof European ancestry  

SciTech Connect

The authors used Southern blot hybridization to study X chromosome-linked color vision genes encoding the apoproteins of red and green visual pigments in 134 unselected Caucasian men. One hundred and thirteen individuals (84.3%) had a normal arrangement of their color vision pigment genes. All had one red pigment gene; the number of green pigment genes ranged from one to five with a mode of two. The frequency of molecular genotypes indicative of normal color vision (84.3%) was significantly lower than had been observed in previous studies of color vision phenotypes. Color vision defects can be due to deletions of red or green pigment genes or due to formation of hybrid genes comprising portions of both red and green pigment genes. Characteristic anomalous patterns were seen in 15 (11.2%) individuals: 7 (5.2%) had patterns characteristic of deuteranomaly, 2 (1.5%) had patterns characteristic of deuteranopia, and 6 (4.5%) had protan patterns. Previously undescribed hybrid gene patterns consisting of both green and red pigment gene fragments in addition to normal red and green genes were observed in another 6 individuals (4.5%). Thus, DNA testing detected anomalous color vision pigment genes at a higher frequency than expected from phenotypic color vision tests.

Drummond-Borg, M.; Deeb, S.S.; Motulsky, A.G. (Univ. of Washington, Seattle (USA))

1989-02-01

342

The Volume Dependence of Cohesive Energy for Nonpolar to Polar Molecules from Molecular Dynamics  

NASA Astrophysics Data System (ADS)

The dependence of the cohesive energy of a fluid on volume, E(V), is critically important in Scatchard-Hildebrand solubility parameter (?) theory, and otherwise modulates the heat of mixing of substances having differing E(V) behavior. Using MD simulations and a high accuracy force field (COMPASS), we have investigated E(V) for a range of small molecules - from those having very low solubility parameters (perfluorobutane) to very large values (ethylene glycol). We find power law behavior, E(V) = CV^-?, over fairly wide ranges of density, but with deviations that result from repulsive interactions at high densities. Electrostatics are shown to play an important role in compressing polar fluids into the repulsive region, thereby reducing the value of the exponent ?. In general, ? decreases with increasing polarity (increasing ?). The simulations are shown to be as reliable as the experimentally measured values.

Eichinger, B. E.

2001-03-01

343

Small molecule interactions with lipid bilayers: a molecular dynamics study of chlorhexidine  

NASA Astrophysics Data System (ADS)

Chlorhexidine presents an interesting modelling challenge with a hydrophobic hexane connecting two biguanides (arginine analogues) and two aromatic rings. We conducted molecular dynamic simulations using the GROMACS simulation software to reproduce the experimental environment of chlorhexidine in a 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC) bilayer to produce atomic-level information. We constructed an all-atom force field of chlorhexidine from the CHARMM36 force field using well established parameters of certain amino acids. Partial charges were treated differently, which were calculated using GAUSSIAN software. We will compare and contrast the results of our model to that of our neutron scattering experiments previously done in our lab.

van Oosten, Brad; Marquardt, Drew; Sternin, Edward; Harroun, Thad

2013-03-01

344

Complex Materials for Molecular Spintronics Applications: Cobalt Bis(dioxolene) Valence Tautomers, from Molecules to Polymers  

NASA Astrophysics Data System (ADS)

Using first principles calculations we predict a complex multifunctional behavior in cobalt bis(dioxolene) valence tautomeric compounds. Molecular spin-state switching is shown to dramatically alter electronic properties and corresponding transport properties. This spin state dependence has been demonstrated for technologically-relevant coordination polymers of valence tautomers as well as for novel conjugated polymers with valence tautomeric functionalization. As a result these materials are proposed as promising candidates for spintronic devices that can couple magnetic bistability with novel electrical and spin conduction properties. Our findings pave the way to the fundamental understanding and future design of active multifunctional organic materials for spintronics applications.

Buongiorno Nardelli, Marco; Calzolari, Arrigo; Chen, Yifeng; Dougherty, Daniel; Shultz, David

2013-03-01

345

Tailoring electronic states of a single molecule using adamantane-based molecular tripods.  

PubMed

Adsorption structures and electronic states of molecular tripods, having a Br atom (BATT) and a ferrocene derivative (Ferrocene-ATT) at the head part of the adamantane-based trithiolate, adsorbed on Au(111) have been investigated using low temperature scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS). We found that BATT and Ferrocene-ATT form self-assembled monolayers (SAMs), and their orderings are identical to one another, which suggests that the adsorption structure of adamantane-based molecular tripods is independent of the type of functional substituent attached to the head part. The electronic states originated from the ferrocene group were confirmed in the STS spectrum of Ferrocene-ATT whereas those are absent in the BATT spectrum. We note that the ferrocene part has few interactions with the Au substrate owing not only to the upright geometry of Ferrocene-ATT but also to the insulative properties of the adamantane base. The STS mapping revealed the spatial distribution of the electronic state of Ferrocene-ATT. PMID:23877197

Katano, Satoshi; Kim, Yousoo; Kitagawa, Toshikazu; Kawai, Maki

2013-07-23

346

Molecular Dynamics of 8-oxoguanine Lesioned B-DNA Molecule - Structure and Energy Analysis  

NASA Astrophysics Data System (ADS)

The molecular dynamics (MD) simulation of DNA mutagenic oxidative lesion - 7,8-dihydro-8-oxoguanine (8-oxoG), complexed with the repair enzyme - human oxoguanine glycosylase 1 (hOGG1) was performed for 1 nanosecond (ns) in order to describe the dynamical process of DNA-enzyme complex formation. After 900 picoseconds of MD the lesioned DNA and enzyme formed a complex that lasted until the end of the simulation at 1 ns. The amino group of arginine 324 was located close to the phosphodiester bond of nucleotide with 8-oxoG enabling chemical reactions between amino acid and lesion. Phosphodiester bond at C5' of 8-oxoG was displaced to the position close to the amino group of arginine 324. In the background simulation of the identical molecular system with the native DNA, neither the complex nor the water mediated hydrogen bond network were observed. The electrostatic energy is supposed to be significant factor causing the disruption of DNA base stacking in DNA duplex and may also to serve as a signal toward the repair enzyme informing on the presence of the lesion.

Pinak, M.; O'Neill, P.; Fujimoto, H.; Nemoto, T.

2004-04-01

347

Nonadiabatic excited-state molecular dynamics modeling of photoinduced dynamics in conjugated molecules.  

PubMed

Nonadiabatic dynamics generally defines the entire evolution of electronic excitations in optically active molecular materials. It is commonly associated with a number of fundamental and complex processes such as intraband relaxation, energy transfer, and light harvesting influenced by the spatial evolution of excitations and transformation of photoexcitation energy into electrical energy via charge separation (e.g., charge injection at interfaces). To treat ultrafast excited-state dynamics and exciton/charge transport we have developed a nonadiabatic excited-state molecular dynamics (NA-ESMD) framework incorporating quantum transitions. Our calculations rely on the use of the Collective Electronic Oscillator (CEO) package accounting for many-body effects and actual potential energy surfaces of the excited states combined with Tully's fewest switches algorithm for surface hopping for probing nonadiabatic processes. This method is applied to model the photoinduced dynamics of distyrylbenzene (a small oligomer of polyphenylene vinylene, PPV). Our analysis shows intricate details of photoinduced vibronic relaxation and identifies specific slow and fast nuclear motions that are strongly coupled to the electronic degrees of freedom, namely, torsion and bond length alternation, respectively. Nonadiabatic relaxation of the highly excited mA(g) state is predicted to occur on a femtosecond time scale at room temperature and on a picosecond time scale at low temperature. PMID:21218841

Nelson, Tammie; Fernandez-Alberti, Sebastian; Chernyak, Vladimir; Roitberg, Adrian E; Tretiak, Sergei

2011-01-10

348

Elicitation and suppression of microbe-associated molecular pattern-triggered immunity in plant?microbe interactions  

Microsoft Academic Search

Summary Recent studies have uncovered fascinating molecular mechanisms underlying plant-microbe interactions that coevolved dynamically. As in animals, the primary plant innate immunity is immediately triggered by the detection of common pathogen- or microbe- associated molecular patterns (PAMPs\\/MAMPs). Different MAMPs are often perceived by distinct cell- surface pattern-recognition receptors (PRRs) and acti- vate convergent intracellular signalling pathways in plant cells for

Ping He; Libo Shan; Jen Sheen

2007-01-01

349

Monte Carlo simulations of ferroelectric crystal growth and molecular electronic structure of atoms and molecules  

NASA Astrophysics Data System (ADS)

In this thesis, we explore two stochastic techniques to study properties of materials in realistic systems. Specifically, the kinetic Monte Carlo (KMC) method is utilized to study the crystal growth process of ferroelectric materials and the quantum Monte Carlo (QMC) approach is used to investigate the ground state properties of atoms and molecules. In the growth simulations, we study the growth rates and chemical ordering of ferroelectric alloys using an electrostatic model with long-range Coulomb interactions. Crystal growth is characterized by thermodynamic processes involving adsorption and evaporation, with solid-on-solid restrictions and excluding diffusion. A KMC algorithm is formulated to simulate this model efficiently in the presence of long-range interactions. The growth process is simulated as a function of temperature, chemical composition, and substrate orientation. We carried out the simulations on two heterovalent binaries, those of the NaCl and the Ba(Mg1/3Nb2/3))O3(BMN) structures. Compared to the simple rocksalt ordered structures, ordered BMN grows only at very low temperatures and only under finely tuned conditions. For materials with tetravalent compositions, such as (1-x)Ba(Mg 1/3Nb2/3))O3 + x BaZrO3 (BMN-BZ), the model does not incorporate tetravalent ions at low-temperature, exhibiting a phase-separated ground state instead. At higher temperatures, tetravalent ions can be incorporated, but the resulting crystals show no chemical ordering in the absence of diffusive mechanisms. In the second part of the thesis, we present results from an auxiliary field quantum Monte Carlo (AFQMC) study of ground state properties, in particular dissociation and ionization energy, of second-row atoms and molecules. The method projects the many-body ground state from a trial wavefunction by random walks in the space of Slater determinants. The Hubbard-Stratonovich transformation is employed to decouple the Coulomb interaction between electrons. A trial wave function is used in the approximation to control the "phase problem". We also carry out Hartree-Fock (HF) and Density Functional Theory (DFT) calculations for comparison to AFQMC results and to serve as starting wavefunctions for our AFQMC calculations. Results of dissociation energy are in excellent agreement with experimental values. Ionization energy errors are somewhat larger than those of other methods. We conclude with a discussion of several possible sources of error as well as a direction for the improvement.

Suewattana, Malliga

350

Diffusion coefficients of small gas molecules in amorphous cis-1,4-polybutadiene estimated by molecular dynamics simulations  

NASA Astrophysics Data System (ADS)

Molecular dynamics (MD) simulations were employed to estimate the diffusion coefficients of small gas molecules (Ar, O2, N2, CO2, and CH4) in amorphous cis-1,4-polybutadiene in the temperature range of 250-400 K. The VT diagram and solubility parameter of the amorphous polymer have been successfully reproduced using a full atomistic potential. Diffusion coefficients were calculated from long NPT MD runs (up to 3 ns) at temperature ranging from 250 up to 400 K. Calculated diffusion coefficients compare well with experimental data as well as previous published work, though a systematic overestimation is found due to the finite-size effect of the model. The influence of various physical and computational parameters on the results is discussed. The diffusion mechanism is examined at the different temperatures of study.

Meunier, M.

2005-10-01

351

Molecular mechanism of SSR128129E, an extracellularly acting, small-molecule, allosteric inhibitor of FGF receptor signaling.  

PubMed

The fibroblast growth factor (FGF)/fibroblast growth factor receptor (FGFR) signaling network plays an important role in cell growth, survival, differentiation, and angiogenesis. Deregulation of FGFR signaling can lead to cancer development. Here, we report an FGFR inhibitor, SSR128129E (SSR), that binds to the extracellular part of the receptor. SSR does not compete with FGF for binding to FGFR but inhibits FGF-induced signaling linked to FGFR internalization in an allosteric manner, as shown by crystallography studies, nuclear magnetic resonance, Fourier transform infrared spectroscopy, molecular dynamics simulations, free energy calculations, structure-activity relationship analysis, and FGFR mutagenesis. Overall, SSR is a small molecule allosteric inhibitor of FGF/FGFR signaling, acting via binding to the extracellular part of the FGFR. PMID:23597563

Herbert, Corentin; Schieborr, Ulrich; Saxena, Krishna; Juraszek, Jarek; De Smet, Frederik; Alcouffe, Chantal; Bianciotto, Marc; Saladino, Giorgio; Sibrac, David; Kudlinzki, Denis; Sreeramulu, Sridhar; Brown, Alan; Rigon, Patrice; Herault, Jean-Pascal; Lassalle, Gilbert; Blundell, Tom L; Rousseau, Frederic; Gils, Ann; Schymkowitz, Joost; Tompa, Peter; Herbert, Jean-Marc; Carmeliet, Peter; Gervasio, Francesco Luigi; Schwalbe, Harald; Bono, Françoise

2013-04-15

352

Simulation of electron paramagnetic resonance spectra of spin-labeled molecules from replica-exchange molecular dynamics  

NASA Astrophysics Data System (ADS)

We report a general approach for the simulation of the electron paramagnetic resonance (EPR) spectra of spin labels attached to peptides and proteins directly from replica-exchange molecular dynamics (REMD) trajectories. Conventional MD trajectories are generally inadequate for the prediction of EPR line shapes since the label can become trapped in one or more of a set of rotameric states, thus preventing both conformational sampling and accurate estimates of the exchange rates between different rotamers. The advantage of using REMD is its ability to provide both efficient conformational sampling and kinetic information for spin-label dynamics. Our approach is illustrated with spin-labeled peptide. This approach to REMD-EPR simulation paves the way for the wider application of MD modeling to the simulation and interpretation of EPR spectra of spin-labeled molecules.

Tyrrell, S.; Oganesyan, V. S.

2013-10-01

353

On the Dimensions of Intramolecularly Crosslinked Polymer Molecules. I. The Synthesis and Chemical Characterization of Intramolecularly Crosslinked Polystyrene Molecules Having a Narrow Distribution of Molecular Weight  

Microsoft Academic Search

The synthesis of intramolecularly crosslinked polystyrene molecules has bee nachieved by controlled chlormethylation of anionic polystyrene. The chlormethyl groups were reacted with n-butylamine and the secondary amine derivative thus produced was crosslinked by reaction with a diisocyanate in dilute solution. Samples were prepared containing a selected number of crosslinks in the range 5 to 150 per polymer molecule. The materials

G. Allen; J. Burgess; S. F. Edwards; D. J. Walsh

1973-01-01

354

Histologic characteristics of non-microsatellite-instable colon adenomas correlate with distinct molecular patterns.  

PubMed

Colon carcinogenesis encompasses the stepwise accumulation of genomic aberrations correlated with the transition of aberrant crypt-adenoma-carcinoma. Recent data have revealed that, in addition to the microsatellite-instable phenotype, the chromosome instability pathway, representing four fifth of the colon carcinoma, could be involved in heterogeneous molecular alterations. Our project was aimed at determining the existence of distinct molecular subtypes in 159 non-microsatellite-instable colon polyps and their correlation with histology and dysplasia, using allelotyping, MGMT promoter gene methylation status, and K-RAS mutation analyses. Allelic imbalance, MGMT methylation, and K-RAS mutations arise in 62%, 39%, and 32% of polyps, respectively. Only 14% of polyps had no alterations. A 2-way hierarchical clustering analysis of the allelic imbalances identified subgroups of polyps according to their allelic imbalance frequency and distribution. Not only tubulovillous adenoma but also high-grade adenomas were correlated with high global allelic imbalance frequency (P = .005 and P = .003), with allelic imbalance at microsatellites targeting chromosomes 1, 6, and 9. In conclusion, the data presented in this study show that a large heterogeneity exists in the molecular patterns of alterations in precancerous colon lesions, favoring different modes of tumor initiation. Therefore, molecular alterations correlated with tubulovillous-type and high-grade dysplasia could represent targets identifying predictive factors of progression. PMID:21238786

Neuville, Agnès; Nicolet, Céline; Meyer, Nicolas; Schneider, Anne; Legrain, Michèle; Brigand, Cécile; Duclos, Bernard; Bachellier, Philippe; Oudet, Pierre; Bellocq, Jean-Pierre; Kedinger, Michèle; Gaub, Marie-Pierre; Guenot, Dominique

2011-02-01

355

Tonal interface to MacroMolecules (TIMMol): A textual and tonal tool for molecular visualization.  

PubMed

We developed the three-dimensional visualization software, Tonal Interface to MacroMolecules or TIMMol, for studying atomic coordinates of protein structures. Key features include audio tones indicating x, y, z location, identification of the cursor location in one-dimensional and three-dimensional space, textual output that can be easily linked to speech or Braille output, and the ability to scroll along the main chain backbone of a protein structure. This program was initially designed for visually impaired users, and it already has shown its effectiveness in helping a blind researcher study X-ray crystal structure data. Subsequently, TIMMol has been enhanced with a graphical display to act as a bridge to ease communication between sighted and visually impaired users as well as to serve users with spatial visualization difficulties. We performed a pilot study to assess the efficacy of the program in conveying three-dimensional information about proteins with and without graphical output to a general scientific audience. Attitudes regarding using TIMMol were assessed using Rasmol, a common visualization package, for comparison. With the use of text and tones exclusively, a majority of users were able to identify specific secondary structure elements, three-dimensional relationships among atoms, and atoms coordinating a ligand. In addition, a majority of users saw benefits in using TIMMol and would recommend it to those having difficulty with standard tools. PMID:21591192

Cordes, Timothy J; Carlson, C Britt; Forest, Katrina T

2008-05-01

356

Molecular dynamics simulation of dextran extension by constant force in single molecule AFM.  

PubMed

The extension of 1-6 polysaccharides has been studied in a series of recent single molecule AFM experiments. For dextran, a key finding was the existence of a plateau in the force-extension curve at forces between 700 and 1000 pN. We studied the extension of the dextran 10-mer under constant force using atomistic simulation with various force fields. All the force fields reproduce the experimental plateau on the force-extension curve. With AMBER94 and AMBER-GLYCAM04 force fields the plateau can be explained by a transition of the glucopyranose rings in the dextran monomers from the chair ((4)C(1)) to the inverted chair ((1)C(4)) conformation while other processes occur at smaller (rotation around C5-C6 bond) or higher (chairs to boat transitions) forces. The CHARMM force field provides a different picture which associates the occurrence of the plateau to chair-boat transitions of the glucopyranose rings. PMID:16950842

Neelov, Igor M; Adolf, David B; McLeish, Tom C B; Paci, Emanuele

2006-09-01

357

Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine.  

PubMed Central

The ability of the four-stranded guanine (G)-DNA motif to incorporate nonstandard guanine analogue bases 6-oxopurine (inosine, I), 6-thioguanine (tG), and 6-thiopurine (tI) has been investigated using large-scale molecular dynamics simulations. The simulations suggest that a G-DNA stem can incorporate inosines without any marked effect on its structure and dynamics. The all-inosine quadruplex stem d(IIII)(4) shows identical dynamical properties as d(GGGG)(4) on the nanosecond time scale, with both molecular assemblies being stabilized by monovalent cations residing in the channel of the stem. However, simulations carried out in the absence of these cations show dramatic differences in the behavior of d(GGGG)(4) and d(IIII)(4). Whereas vacant d(GGGG)(4) shows large fluctuations but does not disintegrate, vacant d(IIII)(4) is completely disrupted within the first nanosecond. This is a consequence of the lack of the H-bonds involving the N2 amino group that is not present in inosine. This indicates that formation of the inosine quadruplex could involve entirely different intermediate structures than formation of the guanosine quadruplex, and early association of cations in this process appears to be inevitable. In the simulations, the incorporation of 6-thioguanine and 6-thiopurine sharply destabilizes four-stranded G-DNA structures, in close agreement with experimental data. The main reason is the size of the thiogroup leading to considerable steric conflicts and expelling the cations out of the channel of the quadruplex stem. The G-DNA stem can accommodate a single thioguanine base with minor perturbations. Incorporation of a thioguanine quartet layer is associated with a large destabilization of the G-DNA stem whereas the all-thioguanine quadruplex immediately collapses.

Stefl, R; Spackova, N; Berger, I; Koca, J; Sponer, J

2001-01-01

358

Wetting on physically patterned solid surfaces: the relevance of molecular dynamics simulations to macroscopic systems.  

PubMed

We used molecular dynamics (MD) simulations to study the wetting of Lennard-Jones cylindrical droplets on surfaces patterned with grooves. By scaling the surface topography parameters with the droplet size, we find that the preferred wetting modes and contact angles become independent of the droplet size. This result is in agreement with a mathematical model for the droplet free energy at small Bond numbers for which the effects of gravity are negligible. The MD contact angles for various wetting modes are in good agreement with those predicted by the mathematical model. We construct phase diagrams of the dependence of the wetting modes observed in the MD simulations on the topography of the surface. Depending on the topographical parameters characterizing the surface, multiple wetting modes can be observed, as is also seen experimentally. Thus, our studies indicate that MD simulations can yield insight into the large-length-scale behavior of droplets on patterned surfaces. PMID:23952673

Shahraz, Azar; Borhan, Ali; Fichthorn, Kristen A

2013-09-03

359

ATOMIC AND MOLECULAR PHYSICS: Interference of dissociating wave packets in the I2 molecule driven by femtosecond laser pulses  

NASA Astrophysics Data System (ADS)

The interference between two dissociating wave packets of the I2 molecule driven by femtosecond laser pulses is theoretically studied by using the time-dependent quantum wave packet method. Both the internuclear distance- and velocity-dependent density functions are calculated and discussed. It is demonstrated that the interference pattern is determined by the phase difference and the delay time between two pump pulses. With two identical pulses with a delay time of 305 fs and a FWHM of 20 fs, more interference fringes can be observed, while with two pump pulses with a delay time of 80 fs and a FWHM of 20 fs, only a few interference fringes can be observed.

Han, Yong-Chang; Hu, Wen-Hui; Yu, Jie; Cong, Shu-Lm

2009-11-01

360

Molecular Population Genetics of the Male and Female Mitochondrial DNA Molecules of the California Sea Mussel, Mytilus californianus  

PubMed Central

The presence of two gender-associated mitochondrial genomes in marine mussels provides a unique opportunity to investigate the dynamics of mtDNA evolution without complications inherent in interspecific comparisons. Here, we assess the relative importance of selection, mutation, and differential constraint in shaping the patterns of polymorphism within and divergence between the male (M) and female (F) mitochondrial genomes of the California sea mussel, Mytilus californianus. Partial sequences were obtained from homologous regions of four genes (nad2, cox1, atp6, and nad5) totaling 2307 bp in length. The M and F mtDNA molecules of M. californianus exhibited extensive levels of nucleotide polymorphism and were more highly diverged than observed in other mytilids (overall Tamura–Nei distances >40%). Consistent with previous studies, the M molecule had significantly higher levels of silent and replacement polymorphism relative to F. Both genomes possessed large numbers of singleton and low-frequency mutations that gave rise to significantly negative Tajima's D values. Mutation-rate scalars estimated for silent and replacement mutations were elevated in the M genome but were not sufficient to account for its higher level of polymorphism. McDonald–Kreitman tests were highly significant at all loci due to excess numbers of fixed replacement mutations between molecules. Strong purifying selection was evident in both genomes in keeping the majority of replacement mutations at low population frequencies but appeared to be slightly relaxed in M. Our results suggest that a reduction in selective constraint acting on the M genome remains the best explanation for its greater levels of polymorphism and faster rate of evolution.

Ort, Brian S.; Pogson, Grant H.

2007-01-01

361

Single-molecule conductance of ?-conjugated rotaxane: new method for measuring stipulated electric conductance of ?-conjugated molecular wire using STM break junction.  

PubMed

An electronic conductance with small fluctuations, which is stipulated in single-molecule junctions, is necessary for the precise control of single-molecule devices. However, the suppression of conductance fluctuations in conventional molecular junctions is intrinsically difficult because the fluctuations are related to the contact fluctuations and molecular motion. In the present study involving experimental and theoretical investigations, it is found that covering a single ?-conjugated wire with an ?-cyclodextrin molecule is a promising technique for suppressing conductance fluctuations. The conductance histogram of the covered molecular junction measured with the scanning tunneling microscope break-junction technique shows that the conductance peak for the covered junction is sharper than that of the uncovered junction. The covering technique thus has two prominent effects: the suppression of intramolecular motion, and the elimination of intermolecular interactions. Theoretical calculations of electronic conductance clearly support these experimental observations. PMID:22223591

Kiguchi, Manabu; Nakashima, Shigeto; Tada, Tomofumi; Watanabe, Satoshi; Tsuda, Susumu; Tsuji, Yasushi; Terao, Jun

2012-01-05

362

Imaging the molecular dimensions and oligomerization of protein molecules at the solid-liquid interface by surface oriented molecular sizing (SOMS) microscopy  

NASA Astrophysics Data System (ADS)

The structure and behavior of proteins at the solid/liquid interface is of great scientific interest. It has application both to fundamental biochemical understanding, as well as to biotechnological purposes. Interfaces play a critical role in many physiological processes. The mechanism of protein adsorption to surfaces is not very well understood. The current model put forth in much of the literature assumes a two step model. In the first step of this model the protein collides with the surface and adsorbs if its energy is sufficient to overcome the free energy of desorption of surface adsorbed solvent. The second step is often assumed to involve significant conformational change of the secondary and tertiary structure of the protein or enzyme, akin to denaturation. This unfolding of the protein would tend to indicate that loss of function would occur concomitantly, but studies have found very little loss in activity upon adsorption for a number of different protein systems. The recent development of the atomic force microscope (AFM) offers another tool for the examination of protein structure at liquid/solid interfaces. For atomically flat crystals the AFM has been used to determine atomic positions to <1 A resolution. In the case of samples with topographic features larger than atoms, the probe tip of the AFM 'convolutes' with the size and shape of surface features. This has hindered the use of AFM for molecular level structural determination of proteins at the liquid/solid interface. The work presented in this dissertation covers the development of the surface oriented molecular sizing (SOMS) technique which makes use of the angstrom height resolution of the AFM and a physically based mathematical framework for the analysis of the height distribution of adsorbed protein molecules. The surface adsorption and orientation (SAO) model is developed using statistical thermodynamics to model the expected height distributions for molecules adsorbed on a surface. The SOMS technique will be shown to be viable through studies of ferritin and concanavalin A (Con A) at the water/mica interface. Using this technique we are able to determine both the three-dimensional size and the oligomerization state of the adsorbed molecules. This technique will then be utilized for the examination of denaturation of Con A at the interface, by a number of mechanisms. Further, the structural and orientational changes in Con A as a function of pH will also be presented. The final chapter of this dissertation will present an extension of these studies to the deposition and structure of Con A thin films on mica.

Waner, Mark Joseph

363

Encapsulation and Diffraction-Pattern-Correction Methods to Reduce the Effect of Damage in X-Ray Diffraction Imaging of Single Biological Molecules  

SciTech Connect

Short and intense x-ray pulses may be used for atomic-resolution diffraction imaging of single biological molecules. Radiation damage and a low signal-to-noise ratio impose stringent pulse requirements. In this Letter, we describe methods for decreasing the damage and improving the signal by encapsulating the molecule in a sacrificial layer (tamper) that reduces atomic motion and by postprocessing the pulse-averaged diffraction pattern to correct for ionization damage. Simulations show that these methods greatly improve the image quality.

Hau-Riege, Stefan P.; London, Richard A.; Chapman, Henry N.; Szoke, Abraham; Timneanu, Nicusor [Lawrence Livermore National Laboratory, P.O. Box 808, Livermore, California 94551 (United States); Biomedical Center, Uppsala University, Box 576, SE 75123, Uppsala (Sweden)

2007-05-11

364

A Molecular Dynamics Study on the Confinement of Carbon Dioxide Molecules in Carbon Nanotubes  

NASA Astrophysics Data System (ADS)

The influence of atmospheric carbon dioxide (CO2) concentration on global warming is considered as one of the primary environmental issues of the past two decades. The main source of CO2 emission is human activity, such as the use of fossil fuels in transportation and industrial plants. Following the release of Kyoto Protocol in 1997, effective ways of controlling CO2 emissions received much attention. As a result, various materials such as activated carbon, zeolites, and carbon nanotubes (CNTs) were investigated for their CO2 adsorbing properties. CNTs were reported to have CO2 adsorption capability twice that of activated carbon, hence they received the most attention. In the current study, single walled carbon nanotubes (SWNTs) were used as one dimensional nanoporous materials and their CO2 adsorption capacity was analyzed with Molecular Dynamics simulations. Results indicated that SWNTs are excellent CO2 adsorbers and their effectiveness increase at low CO2 concentrations. In addition, we showed that by varying temperature, CO2 can be removed from the SWNTs, providing a simple method to reuse SWNTs.

Lazor, Meagan; Rende, Deniz; Baysal, Nihat; Ozisik, Rahmi

2012-02-01

365

Molecular Recombination Between R-Factor Deoxyribonucleic Acid Molecules in Escherichia coli Host Cells  

PubMed Central

Three previously studied R factors were used: 222/R4, controlling transmissible resistance to sulfonamide, streptomycin, chloromycetin, and tetracycline (SUr SMr CMr TCr); 222/R3, a derivative of 222/R4 (now termed 222/R3W) having lost TCr; and R15, controlling infectious resistance to SU and SM only. Two types of derivative R factors were isolated from 222/R4 by serial subculture in Salmonella species. One derivative, termed 222/R1, lost resistance to SU, SM, and CM, and the other, termed 222/R3N, lost only TCr. Each factor was transferred to a standard Escherichia coli K-12 host. Recombinant factors of 222/R4 phenotype were isolated by selection after mixed culture of E. coli (222/R1)+ and (222/R3N)+ strains. Density-gradient equilibrium centrifugation of lysates of E. coli R+ hosts in the presence of ethidium bromide separated R-factor deoxyribonucleic acid (DNA) as a heavy satellite peak which was subjected to electron microscopy or analytical density gradient centrifugation. Each DNA comprised a unimolecular species of circular DNA. The contour of R15 measured 22.3 ?m [equivalent to 46 × 106 atomic mass units (AMU)], and that of 222/R4 measured 33.6 ?m (70 × 106 AMU). 222/R3W appeared to be a point mutant or small deletion of 222/R4 with an almost identical size, whereas 222/R3N had lost a DNA segment of about 3 ?m, and measured 30.3 ?m or 63 × 106 AMU. The 222/R1 factors also appeared to have arisen by loss of DNA from 222/R4, 222/R1A being 22.3 ?m or 46 × 106 AMU, whereas all other 222/R1 factors appeared to be duplicates, measuring 25.6 ?m or 53 × 106 AMU. The DNA from six recombinant factors of R4 phenotype was indistinguishable in size and configuration from the parental 222/R4. In most cases, the number of R-factor copies (present as covalently closed circular molecules) per copy of the E. coli chromosome was less than 2, ranging from 1.2 to 3.3. Images

Nisioka, Taizo; Mitani, Michiko; Clowes, Royston C.

1970-01-01

366

Gate-induced switching and negative differential resistance in a single-molecule transistor: Emergence of fixed and shifting states with molecular length  

NASA Astrophysics Data System (ADS)

The quantum transport of a gated polythiophene nanodevice is analyzed using density functional theory and nonequilibrium Green's function approach. For this typical molecular field effect transistor, we prove the existence of two main features of electronic components, i.e., negative differential resistance and good switching. Ab initio based explanations of these features are provided by distinguishing fixed and shifting conducting states, which are shown to arise from the interface and functional molecule, respectively. The results show that proper functional molecules can be used in conjunction with metallic electrodes to achieve basic electronics functionality at molecular length scales.

Farajian, A. A.; Belosludov, R. V.; Mizuseki, H.; Kawazoe, Y.; Hashizume, T.; Yakobson, B. I.

2007-07-01

367

Limits on the Natural Oxygen-18 Abundance of Cellulose: Intra-molecular Patterns  

NASA Astrophysics Data System (ADS)

The oxygen isotope composition of tree-ring cellulose is an often-invoked quantitative proxy for multiple environmental factors, including paleotemperature, paleohumidity and paleoprecipitation patterns. A broad survey of aerial and aquatic plants reveals an upper limit to the 18O enrichment of cellulose relative to water at the site of cellulose synthesis, which we explain via the comparison of individual oxygen atoms within the cellulose molecule. We collected stems from various geographical regions, extracted stem water and cellulose and determined the oxygen isotope ratios of these two components. The cellulose was hydrolyzed to its glucose moieties and derivatized to determine the oxygen isotope ratios of the oxygens attached to carbon 3, 4, 5, 6 of the glucose moieties, which allowed us to calculate the oxygen isotope ratios of the oxygen attached to the carbon 2 of the glucose moieties. A compilation of results from our collection and from previous publications shows that ?18O values of cellulose increase with ?18O values of stem water only for samples having stem water with ?18O values below -10‰ (SMOW). However, the ?18O values of stem cellulose levels off and remains constant for stems having water with ?18O values greater than -10‰. This pattern suggests a limit on the enrichment of stem (and by inference tree ring) cellulose. This limitation had previously been ascribed to environmental factors affecting leaf water (e.g., humidity, stomatal conductance, solute potential). A compilation of the ?18O values of cellulose from aquatic plants versus that of their ambient water, however, shows the same general pattern which has been previously explained on the basis of evaporation rates and heterogeneities of lake water. We disprove the previous explanations by demonstrating differential isotopic effects on the oxygen atoms of the cellulose molecule. Our observation on the ?18O values of oxygen attached to carbon 2 versus those attached to carbon 3, 4, 5, 6 indicates that the more isotopically enriched are the oxygens attached to carbon 3, 4, 5, 6 -- the more isotopically depleted is the oxygen attached to carbon 2. From these patterns we suggest a biochemical basis for the observed limit in 18O enrichment of cellulose, in contrast to the previously posited environmental influences.

Sternberg, L.; Jahren, H.; Anderson, W.; Pinzon, M. C.

2005-12-01

368

Creating and Using a Consumer Chemical Molecular Graphics Database: The "Molecule of the Day" - A Great Way To Begin Your Lecture  

NASA Astrophysics Data System (ADS)

"The Molecule of the Day" consumer chemical database has been created to allow introductory chemistry students to explore molecular structures of chemicals in household products, and to provide opportunities in molecular modeling for undergraduate chemistry students. Before class begins, an overhead transparency is displayed which shows a three-dimensional molecular structure of a household chemical, and lists relevant features and uses of this chemical. Within answers to questionnaires, students have commented that this molecular graphics database has helped them to visually connect the microscopic structure of a molecule with its physical and chemical properties, as well as its uses in consumer products. It is anticipated that this database will be incorporated into a navigational software package such as Netscape.

Scharberg, Maureen A.; Cox, Oran E.; Barelli, Carl A.

1997-07-01

369

Combining geometric morphometrics, molecular phylogeny, and micropaleontology to assess evolutionary patterns in Mallomonas (Synurophyceae: Heterokontophyta).  

PubMed

Synurophytes, also known as scaled chrysophytes, are ecologically important algae that produce an array of siliceous structures upon which their taxonomy is based. Despite occupying a key position within the photosynthetic heterokonts, the evolutionary history of synurophytes remains poorly constrained. Here, modern and Middle Eocene siliceous scales of the morphotaxon Mallomonas insignis are used as a model to investigate synurophyte evolutionary patterns. Structural details of scale morphology were examined comparatively with scanning electron microscopy and scored for geometric morphometric analyses to assess the stability of shape characters. Although consistent size differences exist (modern scales are larger than Eocene counterparts), the populations cannot be differentiated on the basis of shape or microstructural detail, implying considerable evolutionary stasis in scale morphology. A time-calibrated relaxed molecular clock analysis using a three-gene concatenated data set (27 strains) suggests that the M. insignis lineage predates the available fossil record, having diverged from closest congeneric taxa in the Cretaceous (?94 Ma). However, the molecular analysis also implies that considerable genetic variability is present within several morphotaxa of Mallomonas, implying that substantial genetic variability has arisen despite the retention of uniform scale morphologies, and resulting in the widespread occurrence of cryptic taxa. Results from the synurophyte lineage are consistent with the notion of protracted ghost ranges (>10 Ma) implied by the molecular phylogenies of other algal groups, together pointing to the paucity of the fossil record of these organisms on these timescales. PMID:23331313

Siver, P A; Wolfe, A P; Rohlf, F J; Shin, W; Jo, B Y

2013-01-18

370

Mass spectrometry-based serum proteome pattern analysis in molecular diagnostics of early stage breast cancer  

PubMed Central

Background Mass spectrometric analysis of the blood proteome is an emerging method of clinical proteomics. The approach exploiting multi-protein/peptide sets (fingerprints) detected by mass spectrometry that reflect overall features of a specimen's proteome, termed proteome pattern analysis, have been already shown in several studies to have applicability in cancer diagnostics. We aimed to identify serum proteome patterns specific for early stage breast cancer patients using MALDI-ToF mass spectrometry. Methods Blood samples were collected before the start of therapy in a group of 92 patients diagnosed at stages I and II of the disease, and in a group of age-matched healthy controls (104 women). Serum specimens were purified and the low-molecular-weight proteome fraction was examined using MALDI-ToF mass spectrometry after removal of albumin and other high-molecular-weight serum proteins. Protein ions registered in a mass range between 2,000 and 10,000 Da were analyzed using a new bioinformatic tool created in our group, which included modeling spectra as a sum of Gaussian bell-shaped curves. Results We have identified features of serum proteome patterns that were significantly different between blood samples of healthy individuals and early stage breast cancer patients. The classifier built of three spectral components that differentiated controls and cancer patients had 83% sensitivity and 85% specificity. Spectral components (i.e., protein ions) that were the most frequent in such classifiers had approximate m/z values of 2303, 2866 and 3579 Da (a biomarker built from these three components showed 88% sensitivity and 78% specificity). Of note, we did not find a significant correlation between features of serum proteome patterns and established prognostic or predictive factors like tumor size, nodal involvement, histopathological grade, estrogen and progesterone receptor expression. In addition, we observed a significantly (p = 0.0003) increased level of osteopontin in blood of the group of cancer patients studied (however, the plasma level of osteopontin classified cancer samples with 88% sensitivity but only 28% specificity). Conclusion MALDI-ToF spectrometry of serum has an obvious potential to differentiate samples between early breast cancer patients and healthy controls. Importantly, a classifier built on MS-based serum proteome patterns outperforms available protein biomarkers analyzed in blood by immunoassays.

Pietrowska, Monika; Marczak, Lukasz; Polanska, Joanna; Behrendt, Katarzyna; Nowicka, Elzbieta; Walaszczyk, Anna; Chmura, Aleksandra; Deja, Regina; Stobiecki, Maciej; Polanski, Andrzej; Tarnawski, Rafal; Widlak, Piotr

2009-01-01

371

Spatial and Temporal Expression Patterns of the Epithelial Cell Adhesion Molecule (EpCAM\\/EGP2) in Developing and Adult Kidneys  

Microsoft Academic Search

Background: The epithelial cell adhesion molecule (EpCAM) is expressed by most epithelia and is involved in processes fundamental for morphogenesis, including cell-cell adhesion, proliferation, differentiation, and migration. Previously, a role for EpCAM in pancreatic morphogenesis was confirmed in vitro. Furthermore, changes in the EpCAM expression pattern were found in developing lung and thymus and in the regenerating liver. Therefore, EpCAM

Monika Trzpis; Eliane R. Popa; Pamela M. J. McLaughlin; Harry van Goor; Albertus Timmer; Gerrit W. Bosman; Lou M. F. H. de Leij; Martin C. Harmsen

2007-01-01

372

Density-wave patterns for fermionic dipolar molecules on a square optical lattice: Mean-field-theory analysis  

SciTech Connect

We model a system of ultracold fermionic dipolar molecules on a two-dimensional square lattice. Assuming that the molecules are in their nondegenerate hyperfine ground state, and that the dipole moment is polarized perpendicular to the plane (as in the recent experiments on {sup 40}K-{sup 87}Rb molecules), we approximate these molecules as spinless fermions with long-range repulsive dipolar interactions. We use mean-field theory to obtain the restricted phase diagram as a function of the filling, the strength of interaction, and the temperature. We find a number of ordered density-wave phases in the system, as well as phase separation between these phases. A Monte Carlo analysis shows that the higher-period phases are usually suppressed in the exact solution.

Mikelsons, K.; Freericks, J. K. [Department of Physics, Georgetown University, Washington, DC, 20057 (United States)

2011-04-15

373

The influence of temperature on the synthesis of molecules on icy grain mantles in dense molecular clouds  

NASA Astrophysics Data System (ADS)

Context. Infrared observations show the presence of icy mantles along the line of sight toward young stellar objects (YSOs), where a temperature gradient is expected and indirectly observed. In this environment, icy mantles are affected by ion and UV irradiation. Laboratory experiments show that molecules are formed after irradiation of icy mixtures. However, most of the experiments done so far have been performed in the temperatures range of 10-20 K. Aims: To extend previous work we irradiated some icy mixtures, namely H2O:CO=10:1, H2O:CH4=4:1, and H2O:CO2=3:1 at two different temperatures (12 K and 40 or 60 K) to study the effects of temperature on the synthesis of molecules and the decrease in their parent species after ion irradiation. Methods: The experiments were performed in a high-vacuum chamber (P < 10-7 mbar), where icy samples were irradiated with 30 keV He+ ions and analyzed by a FTIR spectrophotometer. Infrared spectra of the samples were recorded after various steps of irradiation. Results: We found that the temperature affects the behavior of the volatile species (i.e., CO and CH4) during irradiation. As a consequence, the production of molecular species is generally more prevalent at 12 K than at either 40 or 60 K, while the decrease in their parent volatile species is faster at high temperature. Conclusions: We conclude that the behavior of each species depends on the value of its sublimation temperature with respect to the temperature of the sample. If this latter is higher than the sublimation temperature of a given species, then the effects of thermal desorption compete with those due to irradiation.

Garozzo, M.; La Rosa, L.; Kanuchova, Z.; Ioppolo, S.; Baratta, G. A.; Palumbo, M. E.; Strazzulla, G.

2011-04-01

374

Electron spectroscopy (UPS(HeI and II) and metastable impact electron spectroscopy (MIES)) applied to molecular surfaces: the interaction of atoms and molecules with solid water  

Microsoft Academic Search

We report studies of the interaction of atoms and molecules with solid molecular surfaces, water in particular, by combining photoelectron spectroscopy, UPS with HeI and II, and metastable impact electron spectroscopy (MIES). In MIES charge exchange processes of the Auger-type taking place between metastable He atoms and the surface under study are utilized to gain information on their electronic structure.

A. Borodin; O. Höfft; U. Kahnert; V. Kempter; A. Allouche

2004-01-01

375

Adsorption of gas-like molecules to self-aligned square-well fluid channels under confinement of chemically patterned substrates  

NASA Astrophysics Data System (ADS)

To extend the work of binary fluid mixtures and their associated bridge-like structures, the adsorption of gas-like molecules (interacting via hard-sphere potentials) on self-assembled fluid channels was examined. We examined the morphological evolution of an initial random binary mixture under confinement of chemically patterned substrates with strong, long-range preferential attraction to the pure square-well component. Gas-like molecules were presumed to have a weak attraction to the square-well fluid. The morphology and corresponding density profiles revealed the underlying chemical and physical adsorption of gas-like molecules to off-strip voids and to the interface of the self-assembled fluid channels. The entropic effects drive the non-interaction hard-sphere molecules to assemble or reorganize in the voids left between the self-assembled square-well fluids. Such studies can help in the study of formation of nano-liquid structures and enhanced adsorption of gas-like molecules for storage purposes.

Singh, Satya Pal; Singh, Jayant K.; Sharma, Ashutosh

2013-06-01

376

Pattern and predictability in memory formation: From molecular mechanisms to clinical relevance.  

PubMed

Most long-term memories are formed as a consequence of multiple experiences. The temporal spacing of these experiences is of considerable importance: experiences distributed over time (spaced training) are more easily encoded and remembered than either closely spaced experiences, or a single prolonged experience (massed training). In this article, we first review findings from studies in animal model systems that examine the cellular and molecular properties of the neurons and circuits in the brain that underlie training pattern sensitivity during long-term memory (LTM) formation. We next focus on recent findings which have begun to elucidate the mechanisms that support inter-trial interactions during the induction of LTM. Finally, we consider the implications of these findings for developing therapeutic strategies to address questions of direct clinical relevance. PMID:23727358

Philips, Gary T; Kopec, Ashley M; Carew, Thomas J

2013-05-28

377

Interaction between surface migrating pentacene molecules and chemically modified surfaces of silicon oxides studied by pulsed molecular beam scattering  

NASA Astrophysics Data System (ADS)

The interaction between pentacene molecules and organic self-assembling monolayers formed on silicon oxides (SiO2) was studied by measuring the surface scattering time profile of the pulsed molecular beam of pentacene. It was found that the surface residence time (SRT) of pentacene was significantly reduced on a surface treated with hexamethyl silazarane (HMDS) compared with that on a bare SiO2 surface. The activation energies derived from the temperature dependence of the SRT were 24 kJ/mol and 100 kJ/mol for HMDS SiO2 and the bare SiO2, respectively. A surface treated with octadecyltrichlorosilane (OTS) showed SRT values almost the same as those on the bare SiO2 surface, which was due to exposed SiO2 regions on the thermally-degraded OTS SiO2. The growth mechanism with improved quality is due to the shallower adsorption potential and enhanced migration of pentacene by the surface alkylation.

Ichikawa, H.; Koma, A.; Saiki, K.; Shimada, T.

2006-09-01

378

Theoretical study of quantum molecular reaction dynamics and of the effects of intense laser radiation on a diatomic molecule  

SciTech Connect

Within the very broad field of molecular dynamics, we have concentrated on two simple yet important systems. The systems are simple enough so that they are adequately described with a single Born-Oppenheimer potential energy surface and that the dynamics can be calculated accurately. They are important because they give insight into solving more complicated systems. First we discuss H + H/sub 2/ reactive scattering. We present an exact formalism for atom-diatom reactive scattering which avoids the problem of finding a coordinate system appropriate for both reactants and products. We present computational results for collinear H + H/sub 2/ reactive scattering which agree very well with previous calculations. We also present a coupled channel distorted wave Born approximation for atom-diatom reactive scattering which we show is a first order approximation to our exact formalism. We present coupled channel DWBA results for three dimensional H + H/sub 2/ reactive scattering. The second system is an isolated HF molecule in an intense laser field. Using classical trajectories and quantum dynamics, we look at energy absorbed and transition probabilities as a function of the laser pulse time and also averaged over the pulse time. Calculations are performed for both rotating and nonrotating HF. We examine one and two photon absorption about the fundamental frequency, multiphoton absorption, and overtone absorption. 127 references, 31 figures, 12 tables.

Dardi, P.S.

1984-11-01

379

Probe molecules in polymer melts near the glass transition: A molecular dynamics study of chain length effects  

NASA Astrophysics Data System (ADS)

Molecular dynamics simulations of a dense melt of short bead-spring polymer chains containing N=5, 10, or 25 effective monomers are presented and analyzed. Parts of our simulations include also a single dumbbell (N=2) of the same type, which is interpreted to represent a coarse-grained model for a fluorescent probe molecule as used in corresponding experiments. We obtain the mean-square displacements of monomers and chains center of mass, and intermediate incoherent scattering functions of both monomers in the chains and particles in the dumbbells as function of time for a broad regime of temperatures above the critical temperature Tc of mode-coupling theory. For both the chains and the dumbbell, also orientational autocorrelation functions are calculated and for the dumbbell time series for the time evolution of linear dichroism and its autocorrelation function are studied. From both sets of data we find that both the mode-coupling critical temperature Tc (representing the ``cage effect'') and the Vogel-Fulcher temperature T0 (representing the caloric glass transition temperature) systematically increase with chain length. Furthermore, the dumbbell dynamics yields detailed information on the differences in the matrix dynamics that are caused by the chain length variation. Deviations from the Stokes-Einstein relation are discussed, and an outlook to related experiments is given.

Vallée, R. A. L.; Paul, W.; Binder, K.

2010-01-01

380

Versatile piezoelectric pulsed molecular beam source for gaseous compounds and organic molecules with femtomole accuracy for UHV and surface science applications  

SciTech Connect

This note describes the construction of a piezoelectric pulsed molecular beam source based upon a design presented in an earlier work [D. Proch and T. Trickl, Rev. Sci. Instrum. 60, 713 (1988)]. The design features significant modifications that permit the determination of the number of molecules in a beam pulse with an accuracy of 1x10{sup 11} molecules per pulse. The 21 cm long plunger-nozzle setup allows the molecules to be brought to any point of the UHV chamber with very high intensity. Furthermore, besides typical gaseous compounds, also smaller organic molecules with a vapor pressure higher than 0.1 mbar at room temperature may serve as feed material. This makes the new design suitable for various applications in chemical and surface science studies.

Schiesser, Alexander; Schaefer, Rolf [Eduard-Zintl-Institut fuer Anorganische und Physikalische Chemie, Technische Universitaet Darmstadt, Petersenstrasse 20, 64287 Darmstadt (Germany)

2009-08-15

381

Molecular layer deposition of functional thin films for advanced lithographic patterning.  

PubMed

Photoresist materials comprise one of the main challenges faced by lithography to meet the requirements of electronic device size scaling. Here we report for the first time the use of molecular layer deposition (MLD) to produce photoresist materials with controllable placement of functional moieties. Polyurea resists films are deposited by MLD using urea coupling reactions between 1,4-phenylene diisocyanate (PDIC) and ethylenediamine (ED) or 2,2'-(propane-2,2-diylbis(oxy))diethanamine (PDDE) monomers in a layer-by-layer fashion with a linear growth rate, allowing acid-labile groups to be incorporated into the film at well-controlled positions. The films are deposited with stoichiometric compositions and have highly uniform surface morphology as investigated using atomic force microscopy. We show that acid treatment can cleave the backbone of the polyurea film at positions where the acid-labile groups are embedded. We further show that after soaking the polyurea film with photoacid generator (PAG), it acts as a photoresist material and we present several UV patterning demonstrations. This approach presents a new way to make molecularly designed resist films for lithography. PMID:21302918

Zhou, Han; Bent, Stacey F

2011-02-08

382

Identification of Nicotiana benthamiana genes involved in pathogen-associated molecular pattern-triggered immunity.  

PubMed

In order to identify components of pathogen-associated molecular pattern-triggered immunity (PTI) pathways in Nicotiana benthamiana, we conducted a large-scale forward-genetics screen using virus-induced gene silencing and a cell-death-based assay for assessing PTI. The assay relied on four combinations of PTI-inducing nonpathogens and cell-death-causing challenger pathogens and was first validated in plants silenced for FLS2 or BAK1. Over 3,200 genes were screened and 14 genes were identified that, when silenced, compromised PTI as judged by the cell-death-based assay. Further analysis indicated that the 14 genes were not involved in a general cell death response. A subset of the genes was found to act downstream of FLS2-mediated PTI induction, and silencing of three genes compromised production of reactive oxygen species in leaves exposed to flg22. The 14 genes encode proteins with potential functions in defense and hormone signaling, protein stability and degradation, energy and secondary metabolism, and cell wall biosynthesis and provide a new resource to explore the molecular basis for the involvement of these processes in PTI. PMID:20459311

Chakravarthy, Suma; Velásquez, André C; Ekengren, Sophia K; Collmer, Alan; Martin, Gregory B

2010-06-01

383

Patterns of Molecular Evolution in Caenorhabditis Preclude Ancient Origins of Selfing  

PubMed Central

The evolution of self-fertilization can mediate pronounced changes in genomes as a by-product of a drastic reduction in effective population size and the concomitant accumulation of slightly deleterious mutations by genetic drift. In the nematode genus Caenorhabditis, a highly selfing lifestyle has evolved twice independently, thus permitting an opportunity to test for the effects of mode of reproduction on patterns of molecular evolution on a genomic scale. Here we contrast rates of nucleotide substitution and codon usage bias among thousands of orthologous groups of genes in six species of Caenorhabditis, including the classic model organism Caenorhabditis elegans. Despite evidence that weak selection on synonymous codon usage is pervasive in the history of all species in this genus, we find little difference among species in the patterns of codon usage bias and in replacement-site substitution. Applying a model of relaxed selection on codon usage to the C. elegans and C. briggsae lineages suggests that self-fertilization is unlikely to have evolved more than ?4 million years ago, which is less than a quarter of the time since they shared a common ancestor with outcrossing species. We conclude that the profound changes in mating behavior, physiology, and developmental mechanisms that accompanied the transition from an obligately outcrossing to a primarily selfing mode of reproduction evolved in the not-too-distant past.

Cutter, Asher D.; Wasmuth, James D.; Washington, Nicole L.

2008-01-01

384

Molecular dynamics of single-particle impacts predicts phase diagrams for large scale pattern formation.  

PubMed

Energetic particle irradiation can cause surface ultra-smoothening, self-organized nanoscale pattern formation or degradation of the structural integrity of nuclear reactor components. A fundamental understanding of the mechanisms governing the selection among these outcomes has been elusive. Here we predict the mechanism governing the transition from pattern formation to flatness using only parameter-free molecular dynamics simulations of single-ion impacts as input into a multiscale analysis, obtaining good agreement with experiment. Our results overturn the paradigm attributing these phenomena to the removal of target atoms via sputter erosion: the mechanism dominating both stability and instability is the impact-induced redistribution of target atoms that are not sputtered away, with erosive effects being essentially irrelevant. We discuss the potential implications for the formation of a mysterious nanoscale topography, leading to surface degradation, of tungsten plasma-facing fusion reactor walls. Consideration of impact-induced redistribution processes may lead to a new design criterion for stability under irradiation. PMID:21505432

Norris, Scott A; Samela, Juha; Bukonte, Laura; Backman, Marie; Djurabekova, Flyura; Nordlund, Kai; Madi, Charbel S; Brenner, Michael P; Aziz, Michael J

2011-01-01

385

Analysis of molecular expression patterns and integration with other knowledge bases using probabilistic Bayesian network models  

SciTech Connect

How can molecular expression experiments be interpreted with greater than ten to the fourth measurements per chip? How can one get the most quantitative information possible from the experimental data with good confidence? These are important questions whose solutions require an interdisciplinary combination of molecular and cellular biology, computer science, statistics, and complex systems analysis. The explosion of data from microarray techniques present the problem of interpreting the experiments. The availability of large-scale knowledge bases provide the opportunity to maximize the information extracted from these experiments. We have developed new methods of discovering biological function, metabolic pathways, and regulatory networks from these data and knowledge bases. These techniques are applicable to analyses for biomedical engineering, clinical, and fundamental cell and molecular biology studies. Our approach uses probabilistic, computational methods that give quantitative interpretations of data in a biological context. We have selected Bayesian statistical models with graphical network representations as a framework for our methods. As a first step, we use a nave Bayesian classifier to identify statistically significant patterns in gene expression data. We have developed methods which allow us to (a) characterize which genes or experiments distinguish each class from the others, (b) cross-index the resulting classes with other databases to assess biological meaning of the classes, and (c) display a gross overview of cellular dynamics. We have developed a number of visualization tools to convey the results. We report here our methods of classification and our first attempts at integrating the data and other knowledge bases together with new visualization tools. We demonstrate the utility of these methods and tools by analysis of a series of yeast cDNA microarray data and to a set of cancerous/normal sample data from colon cancer patients. We discuss extending our methods to inferring biological pathways and networks using more complex dynamic Bayesian networks.

Moler, Edward J.; Mian, I.S.

2000-03-01

386

Negative feedback regulation of microbe-associated molecular pattern-induced cytosolic Ca 2+ transients by protein phosphorylation  

Microsoft Academic Search

Microbe\\/pathogen-associated molecular patterns (MAMPs\\/PAMPs) often induce rises in cytosolic free Ca2+ concentration ([Ca2+]cyt) and protein phosphorylation. Though they are postulated to play pivotal roles in plant innate immunity, their molecular\\u000a links and the regulatory mechanisms remain largely unknown. To investigate the regulatory mechanisms for MAMP-induced Ca2+ mobilization, we have established a transgenic rice (Oryza sativa) cell line stably expressing apoaequorin,

Takamitsu KurusuHaruyasu; Haruyasu Hamada; Yoshimi Sugiyama; Toshikazu Yagala; Yasuhiro Kadota; Takuya Furuichi; Teruyuki Hayashi; Kenji Umemura; Setsuko Komatsu; Akio Miyao; Hirohiko Hirochika; Kazuyuki Kuchitsu

2011-01-01

387

Multielectron effects in high harmonic generation in N2 and benzene: simulation using a non-adiabatic quantum molecular dynamics approach for laser-molecule interactions.  

PubMed

A mixed quantum-classical approach is introduced which allows the dynamical response of molecules driven far from equilibrium to be modeled. This method is applied to the interaction of molecules with intense, short-duration laser pulses. The electronic response of the molecule is described using time-dependent density functional theory (TDDFT) and the resulting Kohn-Sham equations are solved numerically using finite difference techniques in conjunction with local and global adaptations of an underlying grid in curvilinear coordinates. Using this approach, simulations can be carried out for a wide range of molecules and both all-electron and pseudopotential calculations are possible. The approach is applied to the study of high harmonic generation in N(2) and benzene using linearly polarized laser pulses and, to the best of our knowledge, the results for benzene represent the first TDDFT calculations of high harmonic generation in benzene using linearly polarized laser pulses. For N(2) an enhancement of the cut-off harmonics is observed whenever the laser polarization is aligned perpendicular to the molecular axis. This enhancement is attributed to the symmetry properties of the Kohn-Sham orbital that responds predominantly to the pulse. In benzene we predict that a suppression in the cut-off harmonics occurs whenever the laser polarization is aligned parallel to the molecular plane. We attribute this suppression to the symmetry-induced response of the highest-occupied molecular orbital. PMID:22612091

Dundas, Daniel

2012-05-21

388

Walking molecules.  

PubMed

Movement is intrinsic to life. Biologists have established that most forms of directed nanoscopic, microscopic and, ultimately, macroscopic movements are powered by molecular motors from the dynein, myosin and kinesin superfamilies. These motor proteins literally walk, step by step, along polymeric filaments, carrying out essential tasks such as organelle transport. In the last few years biological molecular walkers have inspired the development of artificial systems that mimic aspects of their dynamics. Several DNA-based molecular walkers have been synthesised and shown to walk directionally along a track upon sequential addition of appropriate chemical fuels. In other studies, autonomous operation--i.e. DNA-walker migration that continues as long as a complex DNA fuel is present--has been demonstrated and sophisticated tasks performed, such as moving gold nanoparticles from place-to-place and assistance in sequential chemical synthesis. Small-molecule systems, an order of magnitude smaller in each dimension and 1000× smaller in molecular weight than biological motor proteins or the walker systems constructed from DNA, have also been designed and operated such that molecular fragments can be progressively transported directionally along short molecular tracks. The small-molecule systems can be powered by light or chemical fuels. In this critical review the biological motor proteins from the kinesin, myosin and dynein families are analysed as systems from which the designers of synthetic systems can learn, ratchet concepts for transporting Brownian substrates are discussed as the mechanisms by which molecular motors need to operate, and the progress made with synthetic DNA and small-molecule walker systems reviewed (142 references). PMID:21416072

von Delius, Max; Leigh, David A

2011-03-17

389

Differential tapasin dependence of MHC class I molecules correlates with conformational changes upon peptide dissociation: A molecular dynamics simulation study  

SciTech Connect

Efficiency of peptide loading to MHC class I molecules in the endoplasmatic reticulum depends on the class I allele and can involve interaction with tapasin and other proteins of the loading complex. Allele HLA-B*4402 (Asp at position 116) depends on tapasin for efficient peptide loading whereas HLA-B*4405 (identical to B*4402 except for Tyr116) can efficiently load peptides in the absence of tapasin. Both alleles adopt very similar structures in the presence of the same peptide. Molecular dynamics (MD) simulations on induced peptide termini dissociation from the ?1/?2 peptide binding domains have been performed to characterize free energy changes and associated structural changes in the two alleles. A smooth free energy change along the distance dissociation coordinate was obtained for N terminus dissociation. A different shape and magnitude of the calculated free energy change and was obtained for induced peptide C terminus dissociation in case of the tapasin independent allele B*4405 compared to B*4402. Structural changes during C terminus dissociation occurred mainly in the first segment of the ?2-helix that flanks the peptide C-terminus binding region (F-pocket) and contacts residue 116. This segment is also close to the proposed tapasin contact region. For B*4402, a stable shift towards an altered open F-pocket structure deviating significantly from the bound form was observed. In contrast, B*4405 showed only a transient opening of the F-pocket followed by relaxation towards a structure close to the bound form upon C terminus dissociation. The greater tendency for peptide-receptive conformation in the absence of peptide combined with a more long-range character of the interactions with the peptide C terminus facilitates peptide binding to B*4405 and could be responsible for the tapasin independence of this allele. A possible role of tapasin in case of HLA-B*4402 and other tapasin-dependent alleles could be the stabilization of a peptide receptive class I conformation.

Sieker, Florian; Straatsma, TP; Springer, Sebastian; Zacharias, Martin W.

2008-08-01

390

Electron beam irradiation for structuring of molecular assemblies  

Microsoft Academic Search

Nontraditional applications of electron beam irradiation for patterning of molecular assemblies are considered. The electron beam can have the following effects on molecular layers: destruction of molecular structure under e-beam irradiation with a successive formation of new molecular system when the irradiation is stopped; variation of the properties of the layer after e-beam irradiation; crosslinking of molecules in the layer

Victor Erokhin; Tatiana Berzina; M. P. Fontana

2004-01-01

391

Diverse redox-active molecules bearing O-, S-, or Se-terminated tethers for attachment to silicon in studies of molecular information storage.  

PubMed

A molecular approach to information storage employs redox-active molecules tethered to an electroactive surface. Attachment of the molecules to electroactive surfaces requires control over the nature of the tether (linker and surface attachment group). We have synthesized a collection of redox-active molecules bearing different linkers and surface anchor groups in free or protected form (hydroxy, mercapto, S-acetylthio, and Se-acetylseleno) for attachment to surfaces such as silicon, germanium, and gold. The molecules exhibit a number of cationic oxidation states, including one (ferrocene), two [zinc(II)porphyrin], three [cobalt(II)porphyrin], or four (lanthanide triple-decker sandwich compound). Electrochemical studies of monolayers of a variety of the redox-active molecules attached to Si(100) electrodes indicate that molecules exhibit a regular mode of attachment (via a Si-X bond, X = O, S, or Se), relatively homogeneous surface organization, and robust reversible electrochemical behavior. The acetyl protecting group undergoes cleavage during the surface deposition process, enabling attachment to silicon via thio or seleno groups without handling free thiols or selenols. PMID:14986994

Balakumar, Arumugham; Lysenko, Andrey B; Carcel, Carole; Malinovskii, Vladimir L; Gryko, Daniel T; Schweikart, Karl-Heinz; Loewe, Robert S; Yasseri, Amir A; Liu, Zhiming; Bocian, David F; Lindsey, Jonathan S

2004-03-01

392

Revealing the molecular structure of single-molecule junctions in different conductance states by fishing-mode tip-enhanced Raman spectroscopy  

PubMed Central

The conductance of single-molecule junctions may be governed by the structure of the molecule in the gap or by the way it bonds with the leads, and the information contained in a Raman spectrum is ideal for examining both. Here we demonstrate that molecule-to-surface bonding may be characterized during electron transport by 'fishing-mode' tip-enhanced Raman spectroscopy (FM-TERS). This technique allows mutually verifiable single-molecule conductance and Raman signals with single-molecule contributions to be acquired simultaneously at room temperature. Density functional theory calculations reveal that the most significant spectral change seen for a gold-4,4?-bipyridine-gold junction results from the deformation of the pyridine ring in contact with the drain electrode at high voltage, and these calculations suggest that a stronger bonding interaction between the molecule and the drain may account for the nonlinear dependence of conductance on bias voltage. FM-TERS will lead to a better understanding of electron-transport processes in molecular junctions.

Liu, Zheng; Ding, Song-Yuan; Chen, Zhao-Bin; Wang, Xiang; Tian, Jing-Hua; Anema, Jason R.; Zhou, Xiao-Shun; Wu, De-Yin; Mao, Bing-Wei; Xu, Xin; Ren, Bin; Tian, Zhong-Qun

2011-01-01

393

Molecular Genetic Features of Polyploidization and Aneuploidization Reveal Unique Patterns for Genome Duplication in Diploid Malus  

PubMed Central

Polyploidization results in genome duplication and is an important step in evolution and speciation. The Malus genome confirmed that this genus was derived through auto-polyploidization, yet the genetic and meiotic mechanisms for polyploidization, particularly for aneuploidization, are unclear in this genus or other woody perennials. In fact the contribution of aneuploidization remains poorly understood throughout Plantae. We add to this knowledge by characterization of eupolyploidization and aneuploidization in 27,542 F1 seedlings from seven diploid Malus populations using cytology and microsatellite markers. We provide the first evidence that aneuploidy exceeds eupolyploidy in the diploid crosses, suggesting aneuploidization is a leading cause of genome duplication. Gametes from diploid Malus had a unique combinational pattern; ova preserved euploidy exclusively, while spermatozoa presented both euploidy and aneuploidy. All non-reduced gametes were genetically heterozygous, indicating first-division restitution was the exclusive mode for Malus eupolyploidization and aneuploidization. Chromosome segregation pattern among aneuploids was non-uniform, however, certain chromosomes were associated for aneuploidization. This study is the first to provide molecular evidence for the contribution of heterozygous non-reduced gametes to fitness in polyploids and aneuploids. Aneuploidization can increase, while eupolyploidization may decrease genetic diversity in their newly established populations. Auto-triploidization is important for speciation in the extant Malus. The features of Malus polyploidization confer genetic stability and diversity, and present heterozygosity, heterosis and adaptability for evolutionary selection. A protocol using co-dominant markers was proposed for accelerating apple triploid breeding program. A path was postulated for evolution of numerically odd basic chromosomes. The model for Malus derivation was considerably revised. Impacts of aneuploidization on speciation and evolution, and potential applications of aneuploids and polyploids in breeding and genetics for other species were evaluated in depth. This study greatly improves our understanding of evolution, speciation, and adaptation of the Malus genus, and provides strategies to exploit polyploidization in other species.

Considine, Michael J.; Wan, Yizhen; D'Antuono, Mario F.; Zhou, Qian; Han, Mingyu; Gao, Hua; Wang, Man

2012-01-01

394

Bacterial regulatory networks--from self-organizing molecules to cell shape and patterns in bacterial communities.  

PubMed

The ESF-EMBO Conference on 'Bacterial Networks' (BacNet13) was held in March 2013, in Pultusk, Poland. It brought together 164 molecular microbiologists, bacterial systems biologists and synthetic biologists to discuss the architecture, function and dynamics of regulatory networks in bacteria. PMID:23846311

Hengge, Regine; Sourjik, Victor

2013-07-12

395

Electronic states of pyrene single crystal and of its single molecule inserted in a molecular vessel of cyclodextrin  

NASA Astrophysics Data System (ADS)

Highly purified single crystals of pyrene were made by a gas phase crystal growth method from 180 times of zone-refined pyrene. The absorption spectra of the single crystal have been transformed from the reflection spectra between 2.5 and 6.5eV at 2, 77K and room temperature. The dry powder of ?-cyclodextrin including pyrene single molecule were prepared in vacuum to investigate the electronic states of the isolated molecule. The absorption spectra of the single molecule show similar spectra to those of the single crystal. The pyrene molecule keeps its electronic character even in the single crystal.

Takahashi, Nobuaki; Gombojav, Bold; Yoshinari, Takehisa; Nagasaka, Shin-Ichiro; Takahashi, Yoshio; Yamamoto, Aishi; Goto, Takenari; Kasuya, Atsuo

2004-10-01

396

Single-Molecule Enzymology  

SciTech Connect

Viewing a movie of an enzyme molecule made from molecular dynamics (MD) simulation, we see incredible details of molecular motions, be it a change of the conformation or the action of a chemical reaction.

Xie, Xiaoliang; Lu, H PETER.

1999-06-04

397

Interaction between the signaling molecules WNT7a and SHH during vertebrate limb development: Dorsal signals regulate anteroposterior patterning  

Microsoft Academic Search

Growth and patterning of the vertebrate limb are controlled by the ridge, posterior mesenchyme, and nonridge ectoderm. Fibroblast growth factor 4 (FGF4) and Sonic hedgehog (SHH) can mediate signaling from the ridge and posterior mesenchyme, respectively. Here we show that dorsal ectoderm is required together with FGF4 to maintain Shh expression. Removal of dorsal ectoderm results in loss of posterior

Yingzi Yang; Lee Niswander

1995-01-01

398

TLR activation regulates damage-associated molecular pattern isoforms released during pyroptosis.  

PubMed

Infection of macrophages by bacterial pathogens can trigger Toll-like receptor (TLR) activation as well as Nod-like receptors (NLRs) leading to inflammasome formation and cell death dependent on caspase-1 (pyroptosis). Complicating the study of inflammasome activation is priming. Here, we develop a priming-free NLRC4 inflammasome activation system to address the necessity and role of priming in pyroptotic cell death and damage-associated molecular pattern (DAMP) release. We find pyroptosis is not dependent on priming and when priming is re-introduced pyroptosis is unaffected. Cells undergoing unprimed pyroptosis appear to be independent of mitochondrial involvement and do not produce inflammatory cytokines, nitrous oxide (NO), or reactive oxygen species (ROS). Nevertheless, they undergo an explosive cell death releasing a chemotactic isoform of the DAMP high mobility group protein box 1 (HMGB1). Importantly, priming through surface TLRs but not endosomal TLRs during pyroptosis leads to the release of a new TLR4-agonist cysteine redox isoform of HMGB1. These results show that pyroptosis is dominant to priming signals and indicates that metabolic changes triggered by priming can affect how cell death is perceived by the immune system. PMID:23222484

Nyström, Sanna; Antoine, Daniel J; Lundbäck, Peter; Lock, John G; Nita, Andreia F; Högstrand, Kari; Grandien, Alf; Erlandsson-Harris, Helena; Andersson, Ulf; Applequist, Steven E