Polyad quantum numbers and multiple resonances in anharmonic vibrational studies of polyatomic molecules.

Science.gov (United States)

Krasnoshchekov, Sergey V; Stepanov, Nikolay F

2013-11-14

In the theory of anharmonic vibrations of a polyatomic molecule, mixing the zero-order vibrational states due to cubic, quartic and higher-order terms in the potential energy expansion leads to the appearance of more-or-less isolated blocks of states (also called polyads), connected through multiple resonances. Such polyads of states can be characterized by a common secondary integer quantum number. This polyad quantum number is defined as a linear combination of the zero-order vibrational quantum numbers, attributed to normal modes, multiplied by non-negative integer polyad coefficients, which are subject to definition for any particular molecule. According to Kellman's method [J. Chem. Phys. 93, 6630 (1990)], the corresponding formalism can be conveniently described using vector algebra. In the present work, a systematic consideration of polyad quantum numbers is given in the framework of the canonical Van Vleck perturbation theory (CVPT) and its numerical-analytic operator implementation for reducing the Hamiltonian to the quasi-diagonal form, earlier developed by the authors. It is shown that CVPT provides a convenient method for the systematic identification of essential resonances and the definition of a polyad quantum number. The method presented is generally suitable for molecules of significant size and complexity, as illustrated by several examples of molecules up to six atoms. The polyad quantum number technique is very useful for assembling comprehensive basis sets for the matrix representation of the Hamiltonian after removal of all non-resonance terms by CVPT. In addition, the classification of anharmonic energy levels according to their polyad quantum numbers provides an additional means for the interpretation of observed vibrational spectra.

Probing strong-field electron-nuclear dynamics of polyatomic molecules using proton motion

International Nuclear Information System (INIS)

Markevitch, Alexei N.; Smith, Stanley M.; Levis, Robert J.; Romanov, Dmitri A.

2007-01-01

Proton ejection during Coulomb explosion is studied for several structure-related organic molecules (anthracene, anthraquinone, and octahydroanthracene) subjected to 800 nm, 60 fs laser pulses at intensities from 0.50 to 4.0x10 14 W cm -2 . The proton kinetic energy distributions are found to be markedly structure specific. The distributions are bimodal for anthracene and octahydroanthracene and trimodal for anthraquinone. Maximum (cutoff) energies of the distributions range from 50 eV for anthracene to 83 eV for anthraquinone. The low-energy mode (∼10 eV) is most pronounced in octahydroanthracene. The dependence of the characteristic features of the distributions on the laser intensity provides insights into molecular specificity of such strong-field phenomena as (i) nonadiabatic charge localization and (ii) field-mediated restructuring of polyatomic molecules polarized by a strong laser field

Prospects of using the second-order perturbation theory of the MP2 type in the theory of electron scattering by polyatomic molecules

Energy Technology Data Exchange (ETDEWEB)

Čársky, Petr [J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.i.i., Dolejškova 3, 18223 Prague 8 (Czech Republic)

2015-01-22

So far the second-order perturbation theory has been only applied to the hydrogen molecule. No application was attempted for another molecule, probably because of technical difficulties of such calculations. The purpose of this contribution is to show that the calculations of this type are now feasible on larger polyatomic molecules even on commonly used computers.

Towards efficient ab initio calculations of electron scattering by polyatomic molecules: II. Efficient evaluation of exchange integrals

Czech Academy of Sciences Publication Activity Database

Čársky, Petr

2010-01-01

Roč. 43, č. 17 (2010), s. 175204 ISSN 0953-4075 R&D Projects: GA MŠk OC09079; GA MŠk(CZ) OC10046; GA ČR GA202/08/0631 Institutional research plan: CEZ:AV0Z40400503 Keywords : ab initio calculations * electron scattering * polyatomic molecules Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.902, year: 2010

Studies of electron collisions with polyatomic molecules using distributed-memory parallel computers

International Nuclear Information System (INIS)

Winstead, C.; Hipes, P.G.; Lima, M.A.P.; McKoy, V.

1991-01-01

Elastic electron scattering cross sections from 5--30 eV are reported for the molecules C 2 H 4 , C 2 H 6 , C 3 H 8 , Si 2 H 6 , and GeH 4 , obtained using an implementation of the Schwinger multichannel method for distributed-memory parallel computer architectures. These results, obtained within the static-exchange approximation, are in generally good agreement with the available experimental data. These calculations demonstrate the potential of highly parallel computation in the study of collisions between low-energy electrons and polyatomic gases. The computational methodology discussed is also directly applicable to the calculation of elastic cross sections at higher levels of approximation (target polarization) and of electronic excitation cross sections

An exact variational method to calculate rovibrational spectra of polyatomic molecules with large amplitude motion

Energy Technology Data Exchange (ETDEWEB)

Yu, Hua-Gen, E-mail: hgy@bnl.gov [Division of Chemistry, Department of Energy and Photon Sciences, Brookhaven National Laboratory, Upton, New York 11973-5000 (United States)

2016-08-28

We report a new full-dimensional variational algorithm to calculate rovibrational spectra of polyatomic molecules using an exact quantum mechanical Hamiltonian. The rovibrational Hamiltonian of system is derived in a set of orthogonal polyspherical coordinates in the body-fixed frame. It is expressed in an explicitly Hermitian form. The Hamiltonian has a universal formulation regardless of the choice of orthogonal polyspherical coordinates and the number of atoms in molecule, which is suitable for developing a general program to study the spectra of many polyatomic systems. An efficient coupled-state approach is also proposed to solve the eigenvalue problem of the Hamiltonian using a multi-layer Lanczos iterative diagonalization approach via a set of direct product basis set in three coordinate groups: radial coordinates, angular variables, and overall rotational angles. A simple set of symmetric top rotational functions is used for the overall rotation whereas a potential-optimized discrete variable representation method is employed in radial coordinates. A set of contracted vibrationally diabatic basis functions is adopted in internal angular variables. Those diabatic functions are first computed using a neural network iterative diagonalization method based on a reduced-dimension Hamiltonian but only once. The final rovibrational energies are computed using a modified Lanczos method for a given total angular momentum J, which is usually fast. Two numerical applications to CH{sub 4} and H{sub 2}CO are given, together with a comparison with previous results.

Computer system for structure recognition of polyatomic molecules by i. r. , n. m. r. , u. v. and m. s. methods

Energy Technology Data Exchange (ETDEWEB)

Gribov, L A; Elyashberg, M E; Serov, V V [USSR Academy of Sciences, Moscow (USSR). V.I. Vernadsky Institute of Geochemistry and Analytical Chemistry

1977-12-15

A system of algorithms and programs for the recognition of the structures of polyatomic molecules by means of i.r., n.m.r., u.v. and mass spectra is described. Examples of structures identified are cited. The results are promising and suggest that the system could be used for the identification of complex organic compounds.

Z-dependent perturbation theory and its application to polyatomic molecules

International Nuclear Information System (INIS)

Galvan, D.H.

1986-01-01

Z-dependent perturbation theory is applied to study the ground states of simple diatomic and triatomic molecules in order to calculate the total third-order energies for these systems. The systems studied are H 2 + , H 2 , H 3 + , HeH +2 , HeH + , and HeH 2 +2 . The total energies are compared with exact energy values, as well as Hartree-Fock values, and the author's results are a considerable improvement over second-order energies for most internuclear distances, and consistently better than Hartree-Fock calculations for all internuclear distances. Compared with variational methods, this method is simpler and more efficient. In order to calculate total energies up to third order, the wave functions necessary will be two-center, one electron or one-center, two-electron wave functions, at most. Hence, the most complicated integrals that have to be performed are three-center, two-electron integrals, and four-center, one-electron integrals, no matter how complex the molecular system. More importantly, the results obtained for the one-electron diatomic molecular ion are directly incorporated into the calculations for polyatomic systems

Communication: General variational approach to nuclear-quadrupole coupling in rovibrational spectra of polyatomic molecules

Science.gov (United States)

Yachmenev, Andrey; Küpper, Jochen

2017-10-01

A general algorithm for computing the quadrupole-hyperfine effects in the rovibrational spectra of polyatomic molecules is presented for the case of ammonia (NH3). The method extends the general variational approach TROVE [J. Mol. Spectrosc. 245, 126-140 (2007)] by adding the extra term in the Hamiltonian that describes the nuclear quadrupole coupling, with no inherent limitation on the number of quadrupolar nuclei in a molecule. We applied the new approach to compute the nitrogen-nuclear-quadrupole hyperfine structure in the rovibrational spectrum of NH143. These results agree very well with recent experimental spectroscopic data for the pure rotational transitions in the ground vibrational and ν2 states and the rovibrational transitions in the ν1, ν3, 2ν4, and ν1 + ν3 bands. The computed hyperfine-resolved rovibrational spectrum of ammonia will be beneficial for the assignment of experimental rovibrational spectra, further detection of ammonia in interstellar space, and studies of the proton-to-electron mass variation.

Collision cross section calculations for polyatomic ions considering rotating diatomic/linear gas molecules

International Nuclear Information System (INIS)

Larriba-Andaluz, Carlos; Hogan, Christopher J.

2014-01-01

Structural characterization of ions in the gas phase is facilitated by measurement of ion collision cross sections (CCS) using techniques such as ion mobility spectrometry. Further information is gained from CCS measurement when comparison is made between measurements and accurately predicted CCSs for model ion structures and the gas in which measurements are made. While diatomic gases, namely molecular nitrogen and air, are being used in CCS measurement with increasingly prevalency, the majority of studies in which measurements are compared to predictions use models in which gas molecules are spherical or non-rotating, which is not necessarily appropriate for diatomic gases. Here, we adapt a momentum transfer based CCS calculation approach to consider rotating, diatomic gas molecule collisions with polyatomic ions, and compare CCS predictions with a diatomic gas molecule to those made with a spherical gas molecular for model spherical ions, tetra-alkylammonium ions, and multiply charged polyethylene glycol ions. CCS calculations are performed using both specular-elastic and diffuse-inelastic collisions rules, which mimic negligible internal energy exchange and complete thermal accommodation, respectively, between gas molecule and ion. The influence of the long range ion-induced dipole potential on calculations is also examined with both gas molecule models. In large part we find that CCSs calculated with specular-elastic collision rules decrease, while they increase with diffuse-inelastic collision rules when using diatomic gas molecules. Results clearly show the structural model of both the ion and gas molecule, the potential energy field between ion and gas molecule, and finally the modeled degree of kinetic energy exchange between ion and gas molecule internal energy are coupled to one another in CCS calculations, and must be considered carefully to obtain results which agree with measurements

NATO Advanced Research Workshop on Dynamics of Polyatomic Van der Waals Complexes

CERN Document Server

Janda, Kenneth

1991-01-01

This publication is the Proceedings of the NATO Advanced Research Workshop (ARW) on the Dynamics of Polyatomic Van der Waals Molecules held at the Chateau de Bonas, Castera-Verduzan, France, from August 21 through August 26, 1989. Van der Waals complexes provide important model problems for understanding energy transfer and dissipation. These processes can be described in great detail for Van der Waals complexes, and the insight gained from such studies can be applied to more complicated chemical problems that are not amenable to detailed study. The workshop concentrated on the current questions and future prospects for extend­ ing our highly detailed knowledge of triatomic Van der Waals molecule dynamics to polyatomic molecules and clusters (one molecule surrounded by several, or up to sev­ eral tens of, atoms). Both experimental and theoretical studies were discussed, with particular emphasis on the dynamical behavior of dissociation as observed in the dis­ tributions of quantum states of the dissociatio...

Energy storage and redistribution in molecules

International Nuclear Information System (INIS)

Hinze, J.

1983-01-01

This book presents information on the following topics: chemistry and spectroscopy of molecules at high levels of excitation; energy and phase randomization in large molecules as probed by laser spectroscopy; intramolecular processes in isolated polyatomic molecules; pulse-probe measurements in low-temperature, low-pressure SF 6 ; the photodissociation dynamics of H 2 S and CF 3 NO; photofragment spectroscopy of the NO 2 dissociation; preparation, laser spectroscopy and predissociation of alkali dimers in supersonic nozzle beams; excited states of small molecules - collisional quenching and photodissociation; quantum-state-resolved scattering of lithium hydride; and molecular negative ions

Polyatomic Trilobite Rydberg Molecules in a Dense Random Gas.

Science.gov (United States)

Luukko, Perttu J J; Rost, Jan-Michael

2017-11-17

Trilobites are exotic giant dimers with enormous dipole moments. They consist of a Rydberg atom and a distant ground-state atom bound together by short-range electron-neutral attraction. We show that highly polar, polyatomic trilobite states unexpectedly persist and thrive in a dense ultracold gas of randomly positioned atoms. This is caused by perturbation-induced quantum scarring and the localization of electron density on randomly occurring atom clusters. At certain densities these states also mix with an s state, overcoming selection rules that hinder the photoassociation of ordinary trilobites.

Variational treatment of electron-polyatomic-molecule scattering calculations using adaptive overset grids

Science.gov (United States)

Greenman, Loren; Lucchese, Robert R.; McCurdy, C. William

2017-11-01

The complex Kohn variational method for electron-polyatomic-molecule scattering is formulated using an overset-grid representation of the scattering wave function. The overset grid consists of a central grid and multiple dense atom-centered subgrids that allow the simultaneous spherical expansions of the wave function about multiple centers. Scattering boundary conditions are enforced by using a basis formed by the repeated application of the free-particle Green's function and potential Ĝ0+V ̂ on the overset grid in a Born-Arnoldi solution of the working equations. The theory is shown to be equivalent to a specific Padé approximant to the T matrix and has rapid convergence properties, in both the number of numerical basis functions employed and the number of partial waves employed in the spherical expansions. The method is demonstrated in calculations on methane and CF4 in the static-exchange approximation and compared in detail with calculations performed with the numerical Schwinger variational approach based on single-center expansions. An efficient procedure for operating with the free-particle Green's function and exchange operators (to which no approximation is made) is also described.

The origin of small and large molecule behavior in the vibrational relaxation of highly excited molecules

International Nuclear Information System (INIS)

Gordon, R.J.

1990-01-01

An explanation is proposed for the qualitatively different types of behavior that have been reported for the vibrational relaxation of highly excited diatomic and polyatomic molecules. It is argued that all of the diatomic molecules that have been studied in bulk relax adiabatically at room temperature. In contrast, large polyatomic molecules have low frequency modes which act at ''doorway'' modes for the rest of the molecules, producing an impulsive relaxation mechanism. The theoretical work of Nesbitt and Hynes showed that impulsive collisions result in an exponential decay of the average vibrational energy of a Morse oscillator, whereas adiabatic collisions produce nonexponential power law behavior. We propose that this result explains a large body of data for the vibrational relaxation of small and large molecules

Multi-layer Lanczos iteration approach to calculations of vibrational energies and dipole transition intensities for polyatomic molecules

International Nuclear Information System (INIS)

Yu, Hua-Gen

2015-01-01

We report a rigorous full dimensional quantum dynamics algorithm, the multi-layer Lanczos method, for computing vibrational energies and dipole transition intensities of polyatomic molecules without any dynamics approximation. The multi-layer Lanczos method is developed by using a few advanced techniques including the guided spectral transform Lanczos method, multi-layer Lanczos iteration approach, recursive residue generation method, and dipole-wavefunction contraction. The quantum molecular Hamiltonian at the total angular momentum J = 0 is represented in a set of orthogonal polyspherical coordinates so that the large amplitude motions of vibrations are naturally described. In particular, the algorithm is general and problem-independent. An application is illustrated by calculating the infrared vibrational dipole transition spectrum of CH based on the ab initio T8 potential energy surface of Schwenke and Partridge and the low-order truncated ab initio dipole moment surfaces of Yurchenko and co-workers. A comparison with experiments is made. The algorithm is also applicable for Raman polarizability active spectra

Thermal ion-molecule reactions in oxygen-containing molecules

International Nuclear Information System (INIS)

Kumakura, Minoru

1981-02-01

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

Cross sections and oscillator strengths for electron-impact excitation of electronic states in polyatomic molecules. Application examples of the BEf- scaling model in optically-allowed transitions

International Nuclear Information System (INIS)

Kato, H.; Kawahara, H.; Hoshino, M.

2009-12-01

Integral cross sections for optically allowed electronic-state excitations by electron impact, are reviewed for polyatomic molecules by applying the Binary-Encounter-Bethe (BEB) scaling model. Following the context of the present review, the scaling model originally proposed by Yong-Ki Kim to determine electron-impact cross sections for ionization of atoms and molecules is also summarized briefly for its wide range of applications [Electron-Impact Cross Section Database, NIST, Y.-K. Kim]. The present report not only focuses on the need for the cross-section data, but also elucidates the verification of the scaling model in the general application for atoms and molecules. Since this report is for a data base, it is summarized for data base users by citing (copying) the descriptions in the original papers and the references within those papers in the style of a textbook. (author)

Molecular extended thermodynamics of rarefied polyatomic gases and wave velocities for increasing number of moments

Energy Technology Data Exchange (ETDEWEB)

Arima, Takashi, E-mail: tks@stat.nitech.ac.jp [Center for Social Contribution and Collaboration, Nagoya Institute of Technology (Japan); Mentrelli, Andrea, E-mail: andrea.mentrelli@unibo.it [Department of Mathematics and Research Center of Applied Mathematics (CIRAM), University of Bologna (Italy); Ruggeri, Tommaso, E-mail: tommaso.ruggeri@unibo.it [Department of Mathematics and Research Center of Applied Mathematics (CIRAM), University of Bologna (Italy)

2014-06-15

Molecular extended thermodynamics of rarefied polyatomic gases is characterized by two hierarchies of equations for moments of a suitable distribution function in which the internal degrees of freedom of a molecule is taken into account. On the basis of physical relevance the truncation orders of the two hierarchies are proven to be not independent on each other, and the closure procedures based on the maximum entropy principle (MEP) and on the entropy principle (EP) are proven to be equivalent. The characteristic velocities of the emerging hyperbolic system of differential equations are compared to those obtained for monatomic gases and the lower bound estimate for the maximum equilibrium characteristic velocity established for monatomic gases (characterized by only one hierarchy for moments with truncation order of moments N) by Boillat and Ruggeri (1997) (λ{sub (N)}{sup E,max})/(c{sub 0}) ⩾√(6/5 (N−1/2 )),(c{sub 0}=√(5/3 k/m T)) is proven to hold also for rarefied polyatomic gases independently from the degrees of freedom of a molecule. -- Highlights: •Molecular extended thermodynamics of rarefied polyatomic gases is studied. •The relation between two hierarchies of equations for moments is derived. •The equivalence of maximum entropy principle and entropy principle is proven. •The characteristic velocities are compared to those of monatomic gases. •The lower bound of the maximum characteristic velocity is estimated.

Molecular extended thermodynamics of rarefied polyatomic gases and wave velocities for increasing number of moments

International Nuclear Information System (INIS)

Arima, Takashi; Mentrelli, Andrea; Ruggeri, Tommaso

2014-01-01

Molecular extended thermodynamics of rarefied polyatomic gases is characterized by two hierarchies of equations for moments of a suitable distribution function in which the internal degrees of freedom of a molecule is taken into account. On the basis of physical relevance the truncation orders of the two hierarchies are proven to be not independent on each other, and the closure procedures based on the maximum entropy principle (MEP) and on the entropy principle (EP) are proven to be equivalent. The characteristic velocities of the emerging hyperbolic system of differential equations are compared to those obtained for monatomic gases and the lower bound estimate for the maximum equilibrium characteristic velocity established for monatomic gases (characterized by only one hierarchy for moments with truncation order of moments N) by Boillat and Ruggeri (1997) (λ (N) E,max )/(c 0 ) ⩾√(6/5 (N−1/2 )),(c 0 =√(5/3 k/m T)) is proven to hold also for rarefied polyatomic gases independently from the degrees of freedom of a molecule. -- Highlights: •Molecular extended thermodynamics of rarefied polyatomic gases is studied. •The relation between two hierarchies of equations for moments is derived. •The equivalence of maximum entropy principle and entropy principle is proven. •The characteristic velocities are compared to those of monatomic gases. •The lower bound of the maximum characteristic velocity is estimated

Multiphoton dissociation of polyatomic molecules

International Nuclear Information System (INIS)

Schulz, P.A.

1979-10-01

The dynamics of infrared multiphoton excitation and dissociation of SF 6 was investigated under collision free conditions by a crossed laser-molecular beam method. In order to understand the excitation mechanism and to elucidate the requirements of laser intensity and energy fluence, a series of experiments were carried out to measure the dissociation yield dependences on energy fluence, vibrational temperature of SF 6 , the pulse duration of the CO 2 laser and the frequency in both one and two laser experiments. Translational energy distributions of the SF 5 dissociation product measured by time of flight and angular distributions and the dissociation lifetime of excited SF 6 as inferred from the observation of secondary dissociation of SF 5 into SF 4 and F during the laser pulse suggest that the dynamics of dissociation of excited molecules is dominated by complete energy randomization and rapid intramolecular energy transfer on a nanosecond timescale, and can be adequately described by RRKM theory. An improved phenomenological model including the initial intensity dependent excitation, a rate equation describing the absorption and stimulated emission of single photons, and the unimolecular dissociation of excited molecules is constructed based on available experimental results. The model shows that the energy fluence of the laser determines the excitation of molecules in the quasi-continuum and the excess energy with which molecules dissociate after the laser pulse. The role played by the laser intensity in multiphoton dissociation is more significant than just that of overcoming the intensity dependent absorption in the lowest levels. 63 references

Half-space problem of unsteady evaporation and condensation of polyatomic gas

Science.gov (United States)

Inaba, Masashi; Yano, Takeru

2016-11-01

On the basis of polyatomic version of the ellipsoidal-statistical Bhatnager-Gross-Krook (ES-BGK) model, we consider time-periodic gas flows in a semi-infinite expanse of an initially equilibrium polyatomic gas (methanol) bounded by its planar condensed phase. The kinetic boundary condition at the vapor-liquid interface is assumed to be the complete condensation condition with periodically time-varying macroscopic variables (temperature, saturated vapor density and velocity of the interface), and the boundary condition at infinity is the local equilibrium distribution function. The time scale of variation of macroscopic variables is assumed to be much larger than the mean free time of gas molecules, and the variations of those from a reference state are assumed to be sufficiently small. We numerically investigate thus formulated time-dependent half-space problem for the polyatomic version of linearized ES-BGK model equation with the finite difference method for the case of the Strouhal number Sh=0.01 and 0.1. It is shown that the amplitude of the mass flux at the interface is the maximum, and the phase difference in time between the mass flux and v∞ - vℓ (v∞: vapor velocity at infinity, vℓ: velocity of the vapor-liquid interface) is the minimum absolute value, when the phase difference in time between the liquid surface temperature (the saturated vapor density) and the velocity of interface is close to zero.

Wave equation of a nonlinear triatomic molecule and the adiabatic correction to the Born--Oppenheimer approximation

International Nuclear Information System (INIS)

Bardo, R.D.; Wolfsberg, M.

1977-01-01

The wave equation for a nonlinear polyatomic molecule is formulated in molecule-fixed coordinates by a method originally due to Hirschfelder and Wigner. Application is made to a triatomic molecule, and the wave equation is explicitly presented in a useful molecule-fixed coordinate system. The formula for the adiabatic correction to the Born--Oppenheimer approximation for a triatomic molecule is obtained. The extension of the present formulation to larger polyatomic molecules is pointed out. Some terms in the triatomic molecule wave equation are discussed in detail

Sequential nonadiabatic excitation of large molecules and ions driven by strong laser fields

International Nuclear Information System (INIS)

Markevitch, Alexei N.; Levis, Robert J.; Romanov, Dmitri A.; Smith, Stanley M.; Schlegel, H. Bernhard; Ivanov, Misha Yu.

2004-01-01

Electronic processes leading to dissociative ionization of polyatomic molecules in strong laser fields are investigated experimentally, theoretically, and numerically. Using time-of-flight ion mass spectroscopy, we study the dependence of fragmentation on laser intensity for a series of related molecules and report regular trends in this dependence on the size, symmetry, and electronic structure of a molecule. Based on these data, we develop a model of dissociative ionization of polyatomic molecules in intense laser fields. The model is built on three elements: (i) nonadiabatic population transfer from the ground electronic state to the excited-state manifold via a doorway (charge-transfer) transition; (ii) exponential enhancement of this transition by collective dynamic polarization of all electrons, and (iii) sequential energy deposition in both neutral molecules and resulting molecular ions. The sequential nonadiabatic excitation is accelerated by a counterintuitive increase of a large molecule's polarizability following its ionization. The generic theory of sequential nonadiabatic excitation forms a basis for quantitative description of various nonlinear processes in polyatomic molecules and ions in strong laser fields

A simple model for correcting the zero point energy problem in classical trajectory simulations of polyatomic molecules

International Nuclear Information System (INIS)

Miller, W.H.; Hase, W.L.; Darling, C.L.

1989-01-01

A simple model is proposed for correcting problems with zero point energy in classical trajectory simulations of dynamical processes in polyatomic molecules. The ''problems'' referred to are that classical mechanics allows the vibrational energy in a mode to decrease below its quantum zero point value, and since the total energy is conserved classically this can allow too much energy to pool in other modes. The proposed model introduces hard sphere-like terms in action--angle variables that prevent the vibrational energy in any mode from falling below its zero point value. The algorithm which results is quite simple in terms of the cartesian normal modes of the system: if the energy in a mode k, say, decreases below its zero point value at time t, then at this time the momentum P k for that mode has its sign changed, and the trajectory continues. This is essentially a time reversal for mode k (only exclamation point), and it conserves the total energy of the system. One can think of the model as supplying impulsive ''quantum kicks'' to a mode whose energy attempts to fall below its zero point value, a kind of ''Planck demon'' analogous to a Brownian-like random force. The model is illustrated by application to a model of CH overtone relaxation

Mechanism and models for collisional energy transfer in highly excited large polyatomic molecules

International Nuclear Information System (INIS)

Gilbert, R. G.

1995-01-01

Collisional energy transfer in highly excited molecules (say, 200-500 kJ mol -1 above the zero-point energy of reactant, or of product, for a recombination reaction) is reviewed. An understanding of this energy transfer is important in predicting and interpreting the pressure dependence of gas-phase rate coefficients for unimolecular and recombination reactions. For many years it was thought that this pressure dependence could be calculated from a single energy-transfer quantity, such as the average energy transferred per collision. However, the discovery of 'super collisions' (a small but significant fraction of collisions which transfer abnormally large amounts of energy) means that this simplistic approach needs some revision. The 'ordinary' (non-super) component of the distribution function for collisional energy transfer can be quantified either by empirical models (e.g., an exponential-down functional form) or by models with a physical basis, such as biased random walk (applicable to monatomic or diatomic collision partners) or ergodic (for polyatomic collision partners) treatments. The latter two models enable approximate expressions for the average energy transfer to be estimated from readily available molecular parameters. Rotational energy transfer, important for finding the pressure dependence for recombination reactions, can for these purposes usually be taken as transferring sufficient energy so that the explicit functional form is not required to predict the pressure dependence. The mechanism of 'ordinary' energy transfer seems to be dominated by low-frequency modes of the substrate, whereby there is sufficient time during a vibrational period for significant energy flow between the collision partners. Super collisions may involve sudden energy flow as an outer atom of the substrate is squashed between the substrate and the bath gas, and then is moved away from the interaction by large-amplitude motion such as a ring vibration or a rotation; improved

Theoretical study of molecular vibration and Application to linear triatomic molecules: case of OCS

International Nuclear Information System (INIS)

Andrianavalomahefa, A.

2014-01-01

Our aim is to give a theoretical approach to the calculation of vibrational energy levels of polyatomic molecules. By using matrix calculation, we have to solve an eigenvalue equation that gives normal vibration frequencies of the system. A basis change introduces normal coordinates of vibration, which diagonalize the Hamiltonian. The harmonic approximation gives a rough evaluation of parameters which describe the system. Then, we introduce nonlinear terms to take into account the anharmonicity of interatomic bounds. Morse oscillator gives good approximation for diatomic molecules. We consider cubic and quartic potential terms for polyatomic molecules. We treat the problem both in classical and quantum approach. The results thus obtained are applied to study longitudinal vibration of carbonyl sulfide. [fr

Wave packet formulation of the boomerang model for resonant electron--molecule scattering

International Nuclear Information System (INIS)

McCurdy, C.W.; Turner, J.L.

1983-01-01

A time-dependent formulation of the boomerang model for resonant electron--molecule scattering is presented in terms of a wave packet propagating on the complex potential surface of the metastable anion. The results of calculations using efficient semiclassical techniques for propagating the wave packet are found to be in excellent agreement with full quantum-mechanical calculations of vibrational excitation cross sections in e - --N 2 scattering. The application of the wave packet formulation as a computational and conceptual approach to the problem of resonant collisions with polyatomic molecules is discussed in the light of recent wave packet calculations on polyatomic photodissociation and Raman spectra

Controlling the nanoscale morphology of organic films deposited by polyatomic ions

CERN Document Server

Hanley, L; Fuoco, E R; Ahu-Akin, F; Wijesundara, M B J; Li, Maozhen; Tikhonov, A; Schlossman, M

2003-01-01

Hyperthermal polyatomic ion beams can be used to fabricate thin film nanostructures with controlled morphology. Several experiments are described in which mass-selected and non-mass-selected polyatomic ion beams are used to create nanometer thick films with controlled surface and buried interface morphologies. Fluorocarbon and thiophenic films are grown on silicon wafers and/or polystyrene from 5 to 200 eV C sub 3 F sub 5 sup + or C sub 4 H sub 4 S sup + ions, respectively. X-ray photoelectron spectroscopy, atomic force microscopy, X-ray reflectivity, and scanning electron microscopy are utilized to analyze the morphology and chemistry of these films. Polyatomic ions are found to control film morphology on the nanoscale through variation of the incident ion energy, ion structure and/or substrate.

Interference effects during the reradiation of ultrashort electromagnetic pulses by polyatomic systems

Energy Technology Data Exchange (ETDEWEB)

Makarov, D. N.; Matveev, V. I., E-mail: mezon98@mail.ru [Lomonosov Northern (Arctic) Federal University (Russian Federation)

2013-11-15

A theory of the reradiation of ultrashort electromagnetic pulses by arbitrary polyatomic systems of isolated complex atoms has been developed. The technique used allows the spatial inhomogeneity of the field of an ultrashort pulse and photon momenta in reradiation processes to be accurately taken into account. The angular distributions of the reradiation spectra have been obtained for an arbitrary number of atoms in the system. The processes of interference between the photon emission amplitudes are shown to give rise to characteristic “diffraction” maxima. We consider one-dimensional, two-dimensional, and three-dimensional rectangular lattices as examples as well as planar and cylindrical structures as models of planar nanosystems and nanotubes.

Reaction dynamics in polyatomic molecular systems

Energy Technology Data Exchange (ETDEWEB)

Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)

1993-12-01

The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.

Research directed at developing a classical theory to describe isotope separation of polyatomic molecules illuminated by intense infrared radiation. Final report, May 7-September 30, 1979

International Nuclear Information System (INIS)

Lamb, W.E. Jr.

1981-12-01

This final report describes research on the theory of isotope separation produced by the illumination of polyatomic molecules by intense infrared laser radiation. This process is investigated by treating the molecule, sulfur hexafluoride, as a system of seven classical particles that obey the Newtonian equations of motion. A minicomputer is used to integrate these differential equations. The particles are acted on by interatomic forces, and by the time-dependent electric field of the laser. We have a very satisfactory expression for the interaction of the laser and the molecule which is compatible with infrared absorption and spectroscopic data. The interatomic potential is capable of improvement, and progress on this problem is still being made. We have made several computer runs of the dynamical behavior of the molecule using a reasonably good model for the interatomic force law. For the laser parameters chosen, we find that typically the molecule passes quickly through the resonance region into the quasi-continuum and even well into the real continuum before dissociation actually occurs. When viewed on a display terminal, the motions are exceedingly complex. As an aid to the visualization of the process, we have made a number of 16 mm movies depicting a three-dimensional representation of the motion of the seven particles. These show even more clearly the enormous complexity of the motions, and make clear the desirability of finding ways of characterizing the motion in simple ways without giving all of the numerical detail. One of the ways to do this is to introduce statistical parameters such as a temperature associated with the distribution of kinetic energies of the single particle. We have made such an analysis of our data runs, and have found favorable indications that such methods will prove useful in keeping track of the dynamical histories

Polyatomic ions in inductively coupled plasma-mass spectrometry

International Nuclear Information System (INIS)

Ferguson, Jill Wisnewski; Dudley, Timothy J.; Sears, Kyle C.; McIntyre, Sally M.; Gordon, Mark S.; Houk, R.S.

2009-01-01

Several polyatomic ions in inductively coupled plasma-mass spectrometry are studied experimentally and by computational methods. Novel calculations based on spin-restricted open shell second order perturbation theory (ZAPT2) and coupled cluster (CCSD(T)) theory are performed to determine the energies, structures and partition functions of the ions. These values are combined with experimental data to evaluate a dissociation constant and gas kinetic temperature (T gas ) value. In our opinion, the resulting T gas value can sometimes be interpreted to deduce the location where the polyatomic ion of interest is generated. The dissociation of N 2 H + to N 2 + leads to a calculated T gas of 4550 to 4900 K, depending on the computational data used. The COH + to CO + system yields a similar temperature, which is not surprising considering the similar energies and structures of COH + and N 2 H + . The dissociation of H 2 CO + to HCO + leads to a much lower T gas ( 2 COH + to HCOH + generates a T gas value between those from the other H x CO + ions studied here. All of these measured T gas values correspond to formation of extra polyatomic ion in the interface or extraction region. The computations reveal the existence of isomers such as HCO + and COH + , and H 2 CO + and HCOH + , which have virtually the same m/z values and need to be considered in the interpretation of results.

Elastic scattering of low energy electrons by hydrogen molecule

International Nuclear Information System (INIS)

Freitas, L.C.G.; Mu-Tao, L.; Botelho, L.F.

1987-01-01

The coherent version of the Renormalized Multiple-Centre Potential Model (RMPM) has been extended to treat the elastic scattering of low energy electrons by H2 molecule. The intramolecular Multiple Scattering (MS) effect has also been included. The comparison against the experimental data shows that the inclusion of the MS improves significantly with experiment. The extension of the present method to study electron-polyatomic molecule interaction is also discussed. (author) [pt

Electron microscope autoradiography of isolated DNA molecules

International Nuclear Information System (INIS)

Delain, Etienne; Bouteille, Michel

1980-01-01

Autoradiographs of 3 H-thymidine-labelled DNA molecules were observed with an electron microscope. After ten months of exposure significant labelling was obtained with tritiated T7 DNA molecules which had a specific activity of 630,000 cpm/μg. Although isolated DNA molecules were not stretched out to such an extent that they could be rigorously compared to straight 'hot lines', the resolution was estimated and found to be similar to that obtained by autoradiography on thin plastic sections. The H.D. value was of the order of 1600A. From the known specific activity of the macromolecules, it was possible to compare the expected number of disintegrations from the samples to the number of grains obtained on the autoradiograms. This enabled us to calculate 1/ The absolute autoradiographic efficiency and 2/ The per cent ratio of thymidine residues labelled with tritium. These results throw some light on the resolution and sensitivity of electron microscope autoradiography of shadowed isolated macromolecules as compared to thin plastic sections

Molecular eigenstate spectroscopy: Application to the intramolecular dynamics of some polyatomic molecules in the 3000 to 7000 cm{sup {minus}1} region

Energy Technology Data Exchange (ETDEWEB)

Perry, D.S. [Univ. of Akron, OH (United States)

1993-12-01

Intramolecular vibrational redistribution (IVR) appears to be a universal property of polyatomic molecules in energy regions where the vibrational density of states is greater than about 5 to 30 states per cm{sup {minus}1}. Interest in IVR stems from its central importance to the spectroscopy, photochemistry, and reaction kinetics of these molecules. A bright state, {var_phi}{sub s}, which may be a C-H stretching vibration, carries the oscillator strength from the ground state. This bright state may mix with bath rotational-vibrational levels to form a clump of molecular eigenstates, each of which carries a portion of the oscillator strength from the ground state. In this work the authors explicitly resolve transitions to each of these molecular eigenstates. Detailed information about the nature of IVR is contained in the frequencies and intensities of the observed discrete transitions. The primary goal of this research is to probe the coupling mechanisms by which IVR takes place. The most fundamental distinction to be made is between anharmonic coupling which is independent of molecular rotation and rotationally-mediated coupling. The authors are also interested in the rate at which IVR takes place. Measurements are strictly in the frequency domain but information is obtained about the decay of the zero order state, {var_phi}{sub s}, which could be prepared in a hypothetical experiment as a coherent excitation of the clump of molecular eigenstates. As the coherent superposition dephases, the energy would flow from the initially prepared mode into nearby overtones and combinations of lower frequency vibrational modes. The decay of the initially prepared mode is related to a pure sequence infrared absorption spectrum by a Fourier transform.

Capability of LEP-type surfaces to describe noncollinear reactions 2 - Polyatomic systems

CERN Document Server

Espinosa-Garcia, Joaquin

2001-01-01

In this second article of the series, the popular LEP-type surface for collinear reaction paths and a "bent" surface, which involves a saddle point geometry with a nonlinear central angle, were used to examine the capacity of LEP-type surfaces to describe the kinetics and dynamics of noncollinear reaction paths in polyatomic systems. Analyzing the geometries, vibrational frequencies, curvature along the reaction path (to estimate the tunneling effect and the reaction coordinate-bound modes coupling), and the variational transition- state theory thermal rate constants for the NH//3 + O(**3P) reaction, we found that the "collinear" LEP-type and the "bent" surfaces for this polyatomic system show similar behavior, thus allowing a considerable saving in time and computational effort. This agreement is especially encouraging for this polyatomic system because in the Cs symmetry the reaction proceeds via two electronic states of symmetries **3A prime and **3A double prime , which had to be independently calibrated....

Theoretical simulations of atomic and polyatomic bombardment of an organic overlayer on a metallic substrate

CERN Document Server

Krantzman, K D; Delcorte, A; Garrison, B J

2003-01-01

Our previous molecular dynamics simulations on initial test systems have laid the foundation for understanding some of the effects of polyatomic bombardment. In this paper, we describe simulations of the bombardment of a more realistic model system, an overlayer of sec-butyl-terminated polystyrene tetramers on a Ag left brace 1 1 1 right brace substrate. We have used this model system to study the bombardment with Xe and SF sub 5 projectiles at kinetic energies ranging from 0.50 to 5.0 keV. SF sub 5 sputters more molecules than Xe, but a higher percentage of these are damaged rather than ejected intact when the bombarding energy is greater than 0.50 keV. Therefore, at energies comparable to experimental values, the efficiency, measured as the yield-to-damage ratio, is greater with Xe than SF sub 5. Stable and intact molecules are generally produced by upward moving substrate atoms, while fragments are produced by the upward and lateral motion of reflected projectile atoms and fragments from the target molecul...

The importance of Rydberg orbitals in dissociative ionization of small hydrocarbon molecules in intense laser fields.

Science.gov (United States)

Jochim, Bethany; Siemering, R; Zohrabi, M; Voznyuk, O; Mahowald, J B; Schmitz, D G; Betsch, K J; Berry, Ben; Severt, T; Kling, Nora G; Burwitz, T G; Carnes, K D; Kling, M F; Ben-Itzhak, I; Wells, E; de Vivie-Riedle, R

2017-06-30

Much of our intuition about strong-field processes is built upon studies of diatomic molecules, which typically have electronic states that are relatively well separated in energy. In polyatomic molecules, however, the electronic states are closer together, leading to more complex interactions. A combined experimental and theoretical investigation of strong-field ionization followed by hydrogen elimination in the hydrocarbon series C 2 D 2 , C 2 D 4 and C 2 D 6 reveals that the photofragment angular distributions can only be understood when the field-dressed orbitals rather than the field-free orbitals are considered. Our measured angular distributions and intensity dependence show that these field-dressed orbitals can have strong Rydberg character for certain orientations of the molecule relative to the laser polarization and that they may contribute significantly to the hydrogen elimination dissociative ionization yield. These findings suggest that Rydberg contributions to field-dressed orbitals should be routinely considered when studying polyatomic molecules in intense laser fields.

Coincidence imaging of polyatomic molecules via laser-induced Coulomb explosion

International Nuclear Information System (INIS)

Gagnon, J; Corkum, P B; Bhardwaj, V R; Lee, Kevin F; Rayner, D M

2008-01-01

We extend laser-induced Coulomb explosion imaging to retrieve the structure of the five-atom dichloromethane (CH 2 Cl 2 ) molecule by developing coincidence imaging and geometry optimization techniques. By detecting all five atoms in coincidence, we show that, from the measured velocity vectors, the geometry of the molecules can be reconstructed.

Double differential cross sections for methane molecules at intermediate energies

International Nuclear Information System (INIS)

Yavuz, Murat; Ozer, Zehra Nur; Ulu, Melike; Dogan, Mevlut; Okumus, Nimet; Sahlaoui, Mohammed; Benmansour, Houda; Bouamoud, Mammar

2014-01-01

Double differential cross sections (DDCS) can be obtained by the measurements of energy and angular distributions of one of the two outgoing electrons by a detector. In this pespective, we used methane molecule as a target that is reasonable to expect to understand ionization mechanisms of polyatomic molecular systems.

Boron- and iron-bearing molecules in laser-induced plasma

Energy Technology Data Exchange (ETDEWEB)

Gaft, M.; Nagli, L.; Eliezer, N.; Groisman, Y.

2015-08-01

Boron combines with alkali-earth elements, such as Ca, Mg, and Sr and with oxygen to form molecules in LIP of boron-bearing minerals with strong and characteristic band emission. It may be supposed that those bands are of CaBO{sub 2}, MgBO{sub 2} and SrBO{sub 2} type. Besides, emission of BO, BO{sub 2} and FeO is also detected. - Highlights: • We studied laser-induced breakdown spectra of B with Ca, Mg and Sr in air. • Emission of polyatomic molecules was found. • Molecules of FeO were found in laser-induced plasma in air.

Multiple scattering of ions in polyatomic materials

International Nuclear Information System (INIS)

Eastham, D.A.

1980-01-01

The equations which determine small angle multiple scattering in the thin polyatomic layers are evaluated numerically for certain cases. A simple approximate method for calculating the scattering in terms of an average target charge which is a function of the target thickness is given and compared with the exact numerical value. The results agree to better than 5% over a wide range of target composition and thickness. (orig.)

Research directed at developing a classical theory to describe isotope separation of polyatomic molecules illuminated by intense infrared radiation. Final report, May 7-September 30, 1979, extension December 31, 1979

International Nuclear Information System (INIS)

Lamb, W.E. Jr.

1981-12-01

This final report describes research on the theory of isotope separation produced by the illumination of polyatomic molecules by intense infrared laser radiation. This process is investigated by treating the molecule, sulfur hexafluoride, as a system of seven classical particles that obey the Newtonian equations of motion. A minicomputer is used to integrate these differential equations. The particles are acted on by interatomic forces, and by the time-dependent electric field of the laser. We have a very satisfactory expression for the interaction of the laser and the molecule which is compatible with infrared absorption and spectroscopic data. The interatomic potential is capable of improvement, and progress on this problem is still being made. We have made several computer runs of the dynamical behavior of the molecule using a reasonably good model for the interatomic force law. For the laser parameters chosen, we find that typically the molecule passes quickly through the resonance region into the quasi-continuum and even well into the real continuum before dissociation actually occurs. When viewed on a display terminal, the motions are exceedingly complex. As an aid to the visualization of the process, we have made a number of 16 mm movies depicting a three-dimensional representation of the motion of the seven particles. These show even more clearly the enormous complexity of the motions, and make clear the desirability of finding ways of characterizing the motion in simple ways without giving all of the numerical detail. One of the ways to do this is to introduce statistical parameters such as a temperature associated with the distribution of kinetic energies of the single particle. We have made such an analysis of our data runs, and have found favorable indications that such methods will prove useful in keeping track of the dynamical histories

An On-the-Fly Surface-Hopping Program JADE for Nonadiabatic Molecular Dynamics of Polyatomic Systems: Implementation and Applications.

Science.gov (United States)

Du, Likai; Lan, Zhenggang

2015-04-14

Nonadiabatic dynamics simulations have rapidly become an indispensable tool for understanding ultrafast photochemical processes in complex systems. Here, we present our recently developed on-the-fly nonadiabatic dynamics package, JADE, which allows researchers to perform nonadiabatic excited-state dynamics simulations of polyatomic systems at an all-atomic level. The nonadiabatic dynamics is based on Tully's surface-hopping approach. Currently, several electronic structure methods (CIS, TDHF, TDDFT(RPA/TDA), and ADC(2)) are supported, especially TDDFT, aiming at performing nonadiabatic dynamics on medium- to large-sized molecules. The JADE package has been interfaced with several quantum chemistry codes, including Turbomole, Gaussian, and Gamess (US). To consider environmental effects, the Langevin dynamics was introduced as an easy-to-use scheme into the standard surface-hopping dynamics. The JADE package is mainly written in Fortran for greater numerical performance and Python for flexible interface construction, with the intent of providing open-source, easy-to-use, well-modularized, and intuitive software in the field of simulations of photochemical and photophysical processes. To illustrate the possible applications of the JADE package, we present a few applications of excited-state dynamics for various polyatomic systems, such as the methaniminium cation, fullerene (C20), p-dimethylaminobenzonitrile (DMABN) and its primary amino derivative aminobenzonitrile (ABN), and 10-hydroxybenzo[h]quinoline (10-HBQ).

Electron scattering resonances and dissociative attachment in polyatomic molecules

International Nuclear Information System (INIS)

Olthoff, J.K.

1985-01-01

A relatively new technique, electron transmission spectroscopic, is now being used to investigate the unoccupied valence molecular orbitals of many chemical compounds. Electron-transmission spectroscopy measures the energy of negative ion states that arise from electron capture into unoccupied molecular orbitals. Additional information about the unoccupied orbitals may be obtained if the negative ion decays by way of dissociation. Determination of the identity, kinetic energy, and production rates of stable ion fragments supplies information about the shape and position of the potential energy curves which describe the electronic states of the molecule and the anion. Used together, photoelectron, electron transmission, and dissociation data can produce a complete picture of a molecule's valence electronic structure. For this work, a time-of-flight mass spectrometer was attached to an electron transmission spectrometer to observe negative ion fragments due to dissociative attachment. The mass spectrometer measures the identify and kinetic energy of stable negative ions as a function of incident electron energy. Electron transmission spectra and ion production data were acquired for many compounds in four chemical categories

Validations of CNDOL approximate Hamiltonian as a fast and reliable method to obtain vertical excitation energies in polyatomic systems

International Nuclear Information System (INIS)

Montero-Alejo, Ana L.; Gonzalez-Santana, Susana; Montero-Cabrera, Luis A.; Hernandez-Rodriguez, Erix Wiliam; Fuentes-Montero, Maria Elena; Bunge-Molina, Carlos F.; Gonzalez, Augusto

2008-01-01

Theoretical prediction of vertical excitation energies and an estimation of charge distributions of polyatomic systems can be calculated, through the configuration interaction of single (CIS) excited determinants procedure, with the CNDOL (Complete Neglect of Differential Overlap considering the l azimuthal quantum number) Hamiltonians. This method does not use adjusted parameters to fit experimental data and only employ a priori data on atomic orbitals and simple formulas to substitute large computations of electronic integrals. In this sense, different functions for bi-electron integrals have been evaluated in order to improve the approximate Hamiltonian. The reliability of predictions and theoretical consistence has been tested with a benchmark set of organic molecules that covers important classes of chromophores including polyenes and other unsaturated aliphatic compounds, aromatic, hydrocarbons, heterocycles, carbonyl compounds, and nucleobases. The calculations are done at identical geometries (MP2) with the same basis set (6-31G) for these medium-sized molecules and the obtained results were statistically compared with other analogous methods and experimental data. The accuracy of prediction of each CNDOL vertical transitions energy increases while the active space is more complete allowing the best variational optimization of CIS matrices i.e. molecular excited states. Moreover and due to the feasible computation procedure for large polyatomic systems, the studies have been extended, as a preliminary work, in the field of optoelectronic materials for photovoltaic applications. Hence, the excitation energies of different conjugated Phenyl-cored Thiophene Dendrimers optimized by DFT (Density Functional Theory) were calculated and show good agreement with the experiment data. The predicted charge distribution during the excitation contributes to understand the photophysics process on these kind materials. (Full text)

Rotation driven translational diffusion of polyatomic ions in water: A novel mechanism for breakdown of Stokes-Einstein relation

Science.gov (United States)

Banerjee, Puja; Yashonath, Subramanian; Bagchi, Biman

2017-04-01

While most of the existing theoretical and simulation studies have focused on simple, spherical, halide and alkali ions, many chemically, biologically, and industrially relevant electrolytes involve complex non-spherical polyatomic ions like nitrate, chlorate, and sulfate to name only a few. Interestingly, some polyatomic ions in spite of being larger in size show anomalously high diffusivity and therefore cause a breakdown of the venerable Stokes-Einstein (S-E) relation between the size and diffusivity. Here we report a detailed analysis of the dynamics of anions in aqueous potassium nitrate (KNO3) and aqueous potassium acetate (CH3COOK) solutions. The two ions, nitrate (-NO3) and acetate (CH3-CO2 ), with their similar size show a large difference in diffusivity values. We present evidence that the translational motion of these polyatomic ions is coupled to the rotational motion of the ion. We show that unlike the acetate ion, nitrate ion with a symmetric charge distribution among all periphery oxygen atoms shows a faster rotational motion with large amplitude rotational jumps which enhances its translational motion due to translational-rotational coupling. By creating a family of modified-charge model systems, we have analysed the rotational motion of asymmetric polyatomic ions and the contribution of it to the translational motion. These model systems help clarifying and establishing the relative contribution of rotational motion in enhancing the diffusivity of the nitrate ion over the value predicted by the S-E relation and also over the other polyatomic ions having asymmetric charge distribution like the acetate ion. In the latter case, reduced rotational motion results in lower diffusivity values than those with symmetric charge distribution. We propose translational-rotational coupling as a general mechanism of the breakdown of the S-E relation in the case of polyatomic ions.

Coherent Bichromatic Force Deflection of Molecules

Science.gov (United States)

Kozyryev, Ivan; Baum, Louis; Aldridge, Leland; Yu, Phelan; Eyler, Edward E.; Doyle, John M.

2018-02-01

We demonstrate the effect of the coherent optical bichromatic force on a molecule, the polar free radical strontium monohydroxide (SrOH). A dual-frequency retroreflected laser beam addressing the X˜2Σ+↔A˜2Π1 /2 electronic transition coherently imparts momentum onto a cryogenic beam of SrOH. This directional photon exchange creates a bichromatic force that transversely deflects the molecules. By adjusting the relative phase between the forward and counterpropagating laser beams we reverse the direction of the applied force. A momentum transfer of 70 ℏk is achieved with minimal loss of molecules to dark states. Modeling of the bichromatic force is performed via direct numerical solution of the time-dependent density matrix and is compared with experimental observations. Our results open the door to further coherent manipulation of molecular motion, including the efficient optical deceleration of diatomic and polyatomic molecules with complex level structures.

Direct simulation Monte Carlo modeling of relaxation processes in polyatomic gases

Science.gov (United States)

Pfeiffer, M.; Nizenkov, P.; Mirza, A.; Fasoulas, S.

2016-02-01

Relaxation processes of polyatomic molecules are modeled and implemented in an in-house Direct Simulation Monte Carlo code in order to enable the simulation of atmospheric entry maneuvers at Mars and Saturn's Titan. The description of rotational and vibrational relaxation processes is derived from basic quantum-mechanics using a rigid rotator and a simple harmonic oscillator, respectively. Strategies regarding the vibrational relaxation process are investigated, where good agreement for the relaxation time according to the Landau-Teller expression is found for both methods, the established prohibiting double relaxation method and the new proposed multi-mode relaxation. Differences and applications areas of these two methods are discussed. Consequently, two numerical methods used for sampling of energy values from multi-dimensional distribution functions are compared. The proposed random-walk Metropolis algorithm enables the efficient treatment of multiple vibrational modes within a time step with reasonable computational effort. The implemented model is verified and validated by means of simple reservoir simulations and the comparison to experimental measurements of a hypersonic, carbon-dioxide flow around a flat-faced cylinder.

Direct simulation Monte Carlo modeling of relaxation processes in polyatomic gases

International Nuclear Information System (INIS)

Pfeiffer, M.; Nizenkov, P.; Mirza, A.; Fasoulas, S.

2016-01-01

Relaxation processes of polyatomic molecules are modeled and implemented in an in-house Direct Simulation Monte Carlo code in order to enable the simulation of atmospheric entry maneuvers at Mars and Saturn’s Titan. The description of rotational and vibrational relaxation processes is derived from basic quantum-mechanics using a rigid rotator and a simple harmonic oscillator, respectively. Strategies regarding the vibrational relaxation process are investigated, where good agreement for the relaxation time according to the Landau-Teller expression is found for both methods, the established prohibiting double relaxation method and the new proposed multi-mode relaxation. Differences and applications areas of these two methods are discussed. Consequently, two numerical methods used for sampling of energy values from multi-dimensional distribution functions are compared. The proposed random-walk Metropolis algorithm enables the efficient treatment of multiple vibrational modes within a time step with reasonable computational effort. The implemented model is verified and validated by means of simple reservoir simulations and the comparison to experimental measurements of a hypersonic, carbon-dioxide flow around a flat-faced cylinder

Direct simulation Monte Carlo modeling of relaxation processes in polyatomic gases

Energy Technology Data Exchange (ETDEWEB)

Pfeiffer, M., E-mail: mpfeiffer@irs.uni-stuttgart.de; Nizenkov, P., E-mail: nizenkov@irs.uni-stuttgart.de; Mirza, A., E-mail: mirza@irs.uni-stuttgart.de; Fasoulas, S., E-mail: fasoulas@irs.uni-stuttgart.de [Institute of Space Systems, University of Stuttgart, Pfaffenwaldring 29, D-70569 Stuttgart (Germany)

2016-02-15

Relaxation processes of polyatomic molecules are modeled and implemented in an in-house Direct Simulation Monte Carlo code in order to enable the simulation of atmospheric entry maneuvers at Mars and Saturn’s Titan. The description of rotational and vibrational relaxation processes is derived from basic quantum-mechanics using a rigid rotator and a simple harmonic oscillator, respectively. Strategies regarding the vibrational relaxation process are investigated, where good agreement for the relaxation time according to the Landau-Teller expression is found for both methods, the established prohibiting double relaxation method and the new proposed multi-mode relaxation. Differences and applications areas of these two methods are discussed. Consequently, two numerical methods used for sampling of energy values from multi-dimensional distribution functions are compared. The proposed random-walk Metropolis algorithm enables the efficient treatment of multiple vibrational modes within a time step with reasonable computational effort. The implemented model is verified and validated by means of simple reservoir simulations and the comparison to experimental measurements of a hypersonic, carbon-dioxide flow around a flat-faced cylinder.

Quorum sensing molecules production by nosocomial and soil isolates Acinetobacter baumannii.

Science.gov (United States)

Erdönmez, Demet; Rad, Abbas Yousefi; Aksöz, Nilüfer

2017-12-01

Acinetobacter species remain alive in hospitals on various surfaces, both dry and moist, forming an important source of hospital infections. These bacteria are naturally resistant to many antibiotic classes. Although the role of the quorum sensing system in regulating the virulence factors of Acinetobacter species has not been fully elucidated, it has been reported that they play a role in bacterial biofilm formation. The biofilm formation helps them to survive under unfavorable growth conditions and antimicrobial treatments. It is based on the accumulation of bacterial communication signal molecules in the area. In this study, we compared the bacterial signal molecules of 50 nosocomial Acinetobacter baumannii strain and 20 A. baumannii strain isolated from soil. The signal molecules were detected by the biosensor bacteria (Chromobacterium violaceum 026, Agrobacterium tumefaciens A136, and Agrobacterium tumefaciens NTL1) and their separation was determined by thin-layer chromatography. As a result, it has been found that soil-borne isolates can produce 3-oxo-C8-AHL and C8-AHL, whereas nosocomial-derived isolates can produce long-chain signals such as C10-AHL, C12-AHL, C14-AHL and C16-AHL. According to these results, it is possible to understand that these signal molecules are found in the infection caused by A. baumannii. The inhibition of this signaling molecules in a communication could use to prevent multiple antibiotic resistance of these bacteria.

Ab initio calculations on collisions of low energy electrons with polyatomic molecules

International Nuclear Information System (INIS)

Rescigno, T.N.

1991-01-01

The Kohn variational method is one of simplest, and oldest, techniques for performing scattering calculations. Nevertheless, a number of formal problems, as well as practical difficulties associated with the computation of certain required matrix elements, delayed its application to electron--molecule scattering problems for many years. This paper will describe the recent theoretical and computational developments that have made the ''complex'' Kohn variational method a practical tool for carrying out calculations of low energy electron--molecule scattering. Recent calculations on a number of target molecules will also be summarized. 41 refs., 7 figs

Radiation-induced transformations of isolated organic molecules in solid rare gas matrices

International Nuclear Information System (INIS)

Feldman, V.I.

1998-01-01

Complete text of publication follows. The studies of radiation-chemical behaviour of isolated organic molecules in rigid inert media are of considerable interest for radiation chemistry and general structural chemistry. Previous efforts were limited to the ESR studies of radicals resulting from some small hydrocarbon molecules in frozen rare gas solutions. Recently, we developed an approach to the radiation chemistry of isolated organic molecules using classic matrix isolation procedure for sample preparation and a combination of ESR and IR spectroscopy for characterization of paramagnetic and diamagnetic species resulting form electron irradiation or organic molecules in solid rare gas matrices at 10-15 K. The results obtained reveal high efficiency of energy transfer from rare gas matrix to organic molecules. The total radiation-chemical yields of degradation of organic molecules in argon and xenon matrices were measured directly by IR spectroscopy. The studies of the effect of electron scavengers on the radiolysis of organic molecules in solid rare gases show that the main primary process is positive hole transfer from matrix to additive molecule. ESR spectra of a number of radical cations (alkanes, ethers, arenes) were first characterized in a low-disturbing environment. It was found that the electronic characteristics (IP, polarizability) of the matrix used had crucial effect on trapping and degradation of primary organic radical cations. Using matrices with various IP provides an unique possibility to examine the chemical meaning of excess energy resulting from exothermic positive hole transfer, that is, to follow the fate of excited cations in condensed phase

Accurate and approximate thermal rate constants for polyatomic chemical reactions

International Nuclear Information System (INIS)

Nyman, Gunnar

2007-01-01

In favourable cases it is possible to calculate thermal rate constants for polyatomic reactions to high accuracy from first principles. Here, we discuss the use of flux correlation functions combined with the multi-configurational time-dependent Hartree (MCTDH) approach to efficiently calculate cumulative reaction probabilities and thermal rate constants for polyatomic chemical reactions. Three isotopic variants of the H 2 + CH 3 → CH 4 + H reaction are used to illustrate the theory. There is good agreement with experimental results although the experimental rates generally are larger than the calculated ones, which are believed to be at least as accurate as the experimental rates. Approximations allowing evaluation of the thermal rate constant above 400 K are treated. It is also noted that for the treated reactions, transition state theory (TST) gives accurate rate constants above 500 K. TST theory also gives accurate results for kinetic isotope effects in cases where the mass of the transfered atom is unchanged. Due to neglect of tunnelling, TST however fails below 400 K if the mass of the transferred atom changes between the isotopic reactions

Research Directed at Developing a Classical Theory to Describe Isotope Separation of Polyatomic Molecules Illuminated by Intense Infrared Radiation. Final Report for period May 7, 1979 to September 30, 1979; Extension December 31, 1997

Science.gov (United States)

Lamb, W. E. Jr.

1981-12-01

This final report describes research on the theory of isotope separation produced by the illumination of polyatomic molecules by intense infrared laser radiation. This process is investigated by treating the molecule, sulfur hexafluoride, as a system of seven classical particles that obey the Newtonian equations of motion. A minicomputer is used to integrate these differential equations. The particles are acted on by interatomic forces, and by the time-dependent electric field of the laser. We have a very satisfactory expression for the interaction of the laser and the molecule which is compatible with infrared absorption and spectroscopic data. The interatomic potential is capable of improvement, and progress on this problem is still being made. We have made several computer runs of the dynamical behavior of the molecule using a reasonably good model for the interatomic force law. For the laser parameters chosen, we find that typically the molecule passes quickly through the resonance region into the quasi-continuum and even well into the real continuum before dissociation actually occurs. When viewed on a display terminal, the motions are exceedingly complex. As an aid to the visualization of the process, we have made a number of 16 mm movies depicting a three-dimensional representation of the motion of the seven particles. These show even more clearly the enormous complexity of the motions, and make clear the desirability of finding ways of characterizing the motion in simple ways without giving all of the numerical detail. One of the ways to do this is to introduce statistical parameters such as a temperature associated with the distribution of kinetic energies of the single particle. We have made such an analysis of our data runs, and have found favorable indications that such methods will prove useful in keeping track of the dynamical histories.

The synthesis of complex molecules in interstellar clouds

Science.gov (United States)

Huntress, W. T., Jr.; Mitchell, G. F.

1979-01-01

The abundances of polyatomic molecules that may be formed by CH3(+) radiative association reactions in dense interstellar molecular clouds are reevaluated. The formation of a number of complex interstellar molecules via radiative association reactions involving ionic precursors other than CH3(+) is also investigated; these additional precursors include CH3O(+), CH3CO(+), CH5(+), HCO(+), NO(+), H2CN(+), C2H2(+), and NH3(+). The results indicate that the postulated gas-phase ion-molecule radiative association reactions could potentially explain the synthesis of most of the more complex species observed in dense molecular clouds such as Sgr B2. It is concluded, however, that in order to be conclusive, laboratory data are needed to show whether or not these reactions proceed at the required rates at low temperatures.

Time-Dependent Wave Packet Dynamics Calculations of Cross Sections for Ultracold Scattering of Molecules

Science.gov (United States)

Huang, Jiayu; Liu, Shu; Zhang, Dong H.; Krems, Roman V.

2018-04-01

Because the de Broglie wavelength of ultracold molecules is very large, the cross sections for collisions of molecules at ultracold temperatures are always computed by the time-independent quantum scattering approach. Here, we report the first accurate time-dependent wave packet dynamics calculation for reactive scattering of ultracold molecules. Wave packet dynamics calculations can be applied to molecular systems with more dimensions and provide real-time information on the process of bond rearrangement and/or energy exchange in molecular collisions. Our work thus makes possible the extension of rigorous quantum calculations of ultracold reaction properties to polyatomic molecules and adds a new powerful tool for the study of ultracold chemistry.

On the calculation of internal forces in mechanically stressed polyatomic molecules

International Nuclear Information System (INIS)

Avdoshenko, Stanislav M.; Konda, Sai Sriharsha M.; Makarov, Dmitrii E.

2014-01-01

We discuss how to define and to compute internal forces in a molecule subjected to mechanical stress. Because of the inherently many-body character of intramolecular interactions, internal forces cannot be uniquely defined without specifying a set of internal coordinates used to describe the molecular structure. When such a set is comprised of 3N − 6 interactomic distances (N being the number of atoms) and includes the bond lengths of interest, we show that the associated forces, while satisfying the equation F = ∂V/∂R (where R is the bond length, F is the internal force in this bond, and V is the potential energy of the molecule), can be determined from the molecular geometry alone. We illustrate these ideas using several toy models ranging from small molecules to a graphene sheet and show that the magnitude of the internal force in a bond is not necessarily a good predictor of its strength in response to mechanical loading. At the same time, analysis of internal forces reveals interesting phenomena such as the force multiplication effect, where weak external forces may, e.g., be used to break strong bonds, and offers insight into the catch-bond phenomenon where chemical reactivity is suppressed through application of a force

Positron scattering by molecules: implementation of the C-tilde-functional

International Nuclear Information System (INIS)

Silva Lino, Jorge Luiz da

1995-01-01

In this work, we present a formulation called the C-Functional to study collisions of low-energy positron by molecules. This formalism is based on the Schwinger Multichannel Method for positrons which although being a quite general method (it is applicable to polyatomic molecules and include polarization and multichannel coupling) is limited to the use of trial wavefunctions consisting only of square integrable basis functions (Gaussian Cartesian Function). In principle this is not a problem, considering that the Schwinger type of methods require a good description of the scattering wavefunction only in the region where the potential is non-zero. However, there exist some situations (long range potentials) where the SMC has consequences. The C-functional (CF) consists in writing the wavefunctions as a sum of a plane-wave plus a combination of trial functions (where the combination is variationally determined). The basic difference between the 2 cases (SMC and CF) is the presence in the CF amplitude of the First (FBA) and Second Born terms. Aiming the preservation of important features of the SMG, we have developed general codes (applicable to polyatomic targets) to evaluate these terms. To illustrate the CF method we show elastic cross sections ti He and H 2 . (author)

Application of the R-matrix method to photoionization of molecules.

Science.gov (United States)

Tashiro, Motomichi

2010-04-07

The R-matrix method has been used for theoretical calculation of electron collision with atoms and molecules for long years. The method was also formulated to treat photoionization process, however, its application has been mostly limited to photoionization of atoms. In this work, we implement the R-matrix method to treat molecular photoionization problem based on the UK R-matrix codes. This method can be used for diatomic as well as polyatomic molecules, with multiconfigurational description for electronic states of both target neutral molecule and product molecular ion. Test calculations were performed for valence electron photoionization of nitrogen (N(2)) as well as nitric oxide (NO) molecules. Calculated photoionization cross sections and asymmetry parameters agree reasonably well with the available experimental results, suggesting usefulness of the method for molecular photoionization.

Molecular dynamics study of kinetic boundary condition at an interface between a polyatomic vapor and its condensed phase

OpenAIRE

Ishiyama, Tatsuya; Yano, Takeru; Fujikawa, Shigeo

2004-01-01

The kinetic boundary condition for the Boltzmann equation at an interface between a polyatomic vapor and its liquid phase is investigated by the numerical method of molecular dynamics, with particular emphasis on the functional form of the evaporation part of the boundary condition, including the evaporation coefficient. The present study is an extension of a previous one for argon [Ishiyama, Yano, and Fujikawa, Phys. Fluids 16, 2899 (2004)] to water and methanol, typical examples of polyatom...

One-dimensional treatment of polyatomic crystals by the Laplace transform method

International Nuclear Information System (INIS)

Rosato, A.; Santana, P.H.A.

1976-01-01

The one dimensional periodic potential problem is solved using the Laplace transform method and a condensed expression for the relation E x k and effective mass for one electron in a polyatomic structure is determined. Applications related to the effect of the asymmetry of the potential upon the one dimensional band structure are discussed [pt

Constructing Potential Energy Surfaces for Polyatomic Systems: Recent Progress and New Problems

Directory of Open Access Journals (Sweden)

J. Espinosa-Garcia

2012-01-01

Full Text Available Different methods of constructing potential energy surfaces in polyatomic systems are reviewed, with the emphasis put on fitting, interpolation, and analytical (defined by functional forms approaches, based on quantum chemistry electronic structure calculations. The different approaches are reviewed first, followed by a comparison using the benchmark H + CH4 and the H + NH3 gas-phase hydrogen abstraction reactions. Different kinetics and dynamics properties are analyzed for these reactions and compared with the available experimental data, which permits one to estimate the advantages and disadvantages of each method. Finally, we analyze different problems with increasing difficulty in the potential energy construction: spin-orbit coupling, molecular size, and more complicated reactions with several maxima and minima, which test the soundness and general applicability of each method. We conclude that, although the field of small systems, typically atom-diatom, is mature, there still remains much work to be done in the field of polyatomic systems.

The role of the dynamic pressure in stationary heat conduction of a rarefied polyatomic gas

Energy Technology Data Exchange (ETDEWEB)

Arima, Takashi, E-mail: arima@kanagawa-u.ac.jp [Department of Mechanical Engineering, Faculty of Engineering, Kanagawa University, Yokohama 221-8686 (Japan); Barbera, Elvira, E-mail: ebarbera@unime.it [Department of Mathematics and Computer Science, University of Messina, V.le F. D' Alcontres 31, 98166 Messina (Italy); Brini, Francesca, E-mail: francesca.brini@unibo.it [Department of Mathematics, University of Bologna, via Saragozza 8, 40123 Bologna (Italy); Sugiyama, Masaru, E-mail: sugiyama@nitech.ac.jp [Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555 (Japan)

2014-07-18

The effect of the dynamic pressure (non-equilibrium pressure) on stationary heat conduction in a rarefied polyatomic gas at rest is elucidated by the theory of extended thermodynamics. It is shown that this effect is observable in a non-polytropic gas. Numerical studies are presented for a para-hydrogen gas as a typical example. - Highlights: • Heat transfer problem in polyatomic rarefied gases is studied in different domains. • Non-zero dynamic pressure is predicted in non-polytropic gases. • The effect of dynamic pressure can be observed indirectly in an experiment. • The case of para-hydrogen is analyzed as an example. • Navier–Stokes, Fourier, and Extended Thermodynamics predictions are compared.

X-ray Diffraction from Isolated and Strongly Aligned Gas-Phase Molecules with a Free-Electron Laser

DEFF Research Database (Denmark)

Küpper, Jochen; Stern, Stephan; Holmegaard, Lotte

2014-01-01

We report experimental results on x-ray diffraction of quantum-state-selected and strongly aligned ensembles of the prototypical asymmetric rotor molecule 2,5-diiodobenzonitrile using the Linac Coherent Light Source. The experiments demonstrate first steps toward a new approach to diffractive...... imaging of distinct structures of individual, isolated gas-phase molecules. We confirm several key ingredients of single molecule diffraction experiments: the abilities to detect and count individual scattered x-ray photons in single shot diffraction data, to deliver state-selected, e. g., structural......-isomer-selected, ensembles of molecules to the x-ray interaction volume, and to strongly align the scattering molecules. Our approach, using ultrashort x-ray pulses, is suitable to study ultrafast dynamics of isolated molecules....

Spectroscopic and dynamical studies of highly energized small polyatomic molecules

Energy Technology Data Exchange (ETDEWEB)

Field, R.W.; Silbey, R.J. [Massachusetts Institute of Technology, Cambridge (United States)

1993-12-01

The authors have initiated a program to perform spectroscopic and dynamic studies of small molecules. Large amplitude motions in excited acetylene were discussed along with plans to record the dispersed fluorescence (DF) and the stimulated emission pumping (SEP) spectra. SEP spectra were reported for the formyl radical. A Fourier transform spectrometer was discussed with respect to its ability to probe the structure of radicals. This instrument is capable of performing studies using various techniques such as magnetic rotation spectroscopy and sub-Doppler sideband-OODR Zeman (SOODRZ) spectroscopy.

Why Do Simple Molecules with "Isolated" Phenyl Rings Emit Visible Light?

Science.gov (United States)

Zhang, Haoke; Zheng, Xiaoyan; Xie, Ni; He, Zikai; Liu, Junkai; Leung, Nelson L C; Niu, Yingli; Huang, Xuhui; Wong, Kam Sing; Kwok, Ryan T K; Sung, Herman H Y; Williams, Ian D; Qin, Anjun; Lam, Jacky W Y; Tang, Ben Zhong

2017-11-15

π-Bonds connected with aromatic rings were generally believed as the standard structures for constructing highly efficient fluorophores. Materials without these typical structures, however, exhibited only low fluorescence quantum yields and emitted in the ultraviolet spectral region. In this work, three molecules, namely bis(2,4,5-trimethylphenyl)methane, 1,1,2,2-tetrakis(2,4,5-trimethylphenyl)ethane, and 1,1,2,2-tetraphenylethane, with nonconjugated structures and isolated phenyl rings were synthesized and their photophysical properties were systematically investigated. Interestingly, the emission spectra of these three molecules could be well extended to 600 nm with high solid-state quantum yields of up to 70%. Experimental and theoretical analyses proved that intramolecular through-space conjugation between the "isolated" phenyl rings played an important role for this abnormal phenomenon.

Molecular physics. Theoretical principles and experimental methods

International Nuclear Information System (INIS)

Demtroeder, W.

2005-01-01

This advanced textbook comprehensively explains important principles of diatomic and polyatomic molecules and their spectra in two separate, distinct parts. The first part concentrates on the theoretical aspects of molecular physics, whereas the second part of the book covers experimental techniques, i.e. laser, Fourier, NMR, and ESR spectroscopies, used in the fields of physics, chemistry, biolog, and material science. Appropriate for undergraduate and graduate students in physics and chemistry with a knowledge of atomic physics and familiar with the basics of quantum mechanics. From the contents: - Electronic States of Molecules, - Rotation, Oscillation and Potential Curves of Diatomic Molecules, - The Spectra of Diatomic Molecules, - Molecule Symmetries and Group Theory, - Rotation and Oscillations of Polyatomic Molecules, - Electronic States of Polyatomic Molecules, - The Spectra of Polyatomic Molecules, - Collapse of the Born-Oppenheimer-Approximation, Disturbances in Molecular Spectra, - Molecules in Disturbing Fields, - Van-der-Waals-Molecules and Cluster, - Experimental Techniques in Molecular Physics. (orig.)

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

International Nuclear Information System (INIS)

Kim, Hwa Joong; Kim, Young Sik

2001-01-01

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

Structure of deformable diatomic molecules: a modified n-butane liquid

International Nuclear Information System (INIS)

Jang, Seanea; Kim, Soonchul; Lee, Songhi

2005-01-01

The density functional approximation for polyatomic molecules, which is based on the bridge function of the intermolecular interaction, was developed and applied to investigate the thermodynamic and the structural properties of deformable diatomic molecules. The Percus trick was employed to calculate the uniform structure of modified n-butane. The calculated static correlation functions were used to predict the density behaviors of a modified n-butane liquid at liquid-solid interfaces. The theoretical results show that (i) at low densities, the hypernetted-chain (HNC) equation compares with the density functional approximation based on the bridge function and that (ii) the relative population between the gauche and the trans states strongly affects the liquid structure at liquid-solid interfaces.

Electron ionization of open/closed chain isocarbonic molecules relevant in plasma processing: Theoretical cross sections

International Nuclear Information System (INIS)

Patel, Umang R.; Joshipura, K. N.; Pandya, Siddharth H.; Kothari, Harshit N.

2014-01-01

In this paper, we report theoretical electron impact ionization cross sections from threshold to 2000 eV for isocarbonic open chain molecules C 4 H 6 , C 4 H 8 , C 4 F 6 including their isomers, and closed chain molecules c-C 4 H 8 and c-C 4 F 8 . Theoretical formalism employed presently, viz., Complex Scattering Potential-ionization contribution method has been used successfully for a variety of polyatomic molecules. The present ionization calculations are very important since results available for the studied targets are either scarce or none. Our work affords comparison of C 4 containing hydrocarbon versus fluorocarbon molecules. Comparisons of the present ionization cross sections are made wherever possible, and new ionization data are also presented

Kinetic theory of two-temperature polyatomic plasmas

Science.gov (United States)

Orlac'h, Jean-Maxime; Giovangigli, Vincent; Novikova, Tatiana; Roca i Cabarrocas, Pere

2018-03-01

We investigate the kinetic theory of two-temperature plasmas for reactive polyatomic gas mixtures. The Knudsen number is taken proportional to the square root of the mass ratio between electrons and heavy-species, and thermal non-equilibrium between electrons and heavy species is allowed. The kinetic non-equilibrium framework also requires a weak coupling between electrons and internal energy modes of heavy species. The zeroth-order and first-order fluid equations are derived by using a generalized Chapman-Enskog method. Expressions for transport fluxes are obtained in terms of macroscopic variable gradients and the corresponding transport coefficients are expressed as bracket products of species perturbed distribution functions. The theory derived in this paper provides a consistent fluid model for non-thermal multicomponent plasmas.

Collisions of polyatomic ions with surfaces: incident energy partitioning and chemical reactions

International Nuclear Information System (INIS)

Zabka, J.; Roithova, J.; Dolejsek, Z.; Herman, Z.

2002-01-01

Collision of polyatomic ions with surfaces were investigated in ion-surface scattering experiments to obtain more information on energy partitioning in ion-surface collision and on chemical reactions at surfaces. Mass spectra, translation energy and angular distributions of product ions were measured in dependence on the incident energy and the incident angle of polyatomic projectiles. From these data distributions of energy fractions resulting in internal excitation of the projectile, translation energy of the product ions, and energy absorbed by the surface were determined. The surface investigated were a standard stainless steel surface, covered by hydrocarbons, carbon surfaces at room and elevated temperatures, and several surfaces covered by a self-assembled monolayers (C 12 -hydrocarbon SAM, C 11 -perfluorohydrocarbon SAM, and C 11 hydrocarbon with terminal -COOH group SAM). The main processes observed at collision energies of 10 - 50 eV were: neutralization of the ions at surfaces, inelastic scattering and dissociations of the projectile ions, quasi elastic scattering of the projectile ions, and chemical reactions with the surface material (usually hydrogen-atom transfer reactions). The ion survival factor was estimated to be a few percent for even-electron ions (like protonated ethanol ion, C 2 H 5 O + , CD 5 + ) and about 10 - 10 2 times lower for radical ions (like ethanol and benzene molecular ions, CD 4 + ). In the polyatomic ion -surface energy transfer experiments, the ethanol molecular ion was used as a well-characterized projectile ion. The results with most of the surfaces studied showed in the collision energy range of 13 - 32 eV that most collisions were strongly inelastic with about 6 - 8 % of the incident projectile energy transformed into internal excitation of the projectile (independent of the incident angle) and led partially to its further dissociation in a unimolecular way after the interaction with the surface. The incident energy

Polyatomic ions from a high current ion implanter driven by a liquid metal ion source

Science.gov (United States)

Pilz, W.; Laufer, P.; Tajmar, M.; Böttger, R.; Bischoff, L.

2017-12-01

High current liquid metal ion sources are well known and found their first application as field emission electric propulsion thrusters in space technology. The aim of this work is the adaption of such kind of sources in broad ion beam technology. Surface patterning based on self-organized nano-structures on, e.g., semiconductor materials formed by heavy mono- or polyatomic ion irradiation from liquid metal (alloy) ion sources (LMAISs) is a very promising technique. LMAISs are nearly the only type of sources delivering polyatomic ions from about half of the periodic table elements. To overcome the lack of only very small treated areas by applying a focused ion beam equipped with such sources, the technology taken from space propulsion systems was transferred into a large single-end ion implanter. The main component is an ion beam injector based on high current LMAISs combined with suited ion optics allocating ion currents in the μA range in a nearly parallel beam of a few mm in diameter. Different types of LMAIS (needle, porous emitter, and capillary) are presented and characterized. The ion beam injector design is specified as well as the implementation of this module into a 200 kV high current ion implanter operating at the HZDR Ion Beam Center. Finally, the obtained results of large area surface modification of Ge using polyatomic Bi2+ ions at room temperature from a GaBi capillary LMAIS will be presented and discussed.

Low-energy positron interactions with atoms and molecules

International Nuclear Information System (INIS)

Surko, C M; Gribakin, G F; Buckman, S J

2005-01-01

This paper is a review of low-energy positron interactions with atoms and molecules. Processes of interest include elastic scattering, electronic and vibrational excitation, ionization, positronium formation and annihilation. An overview is presented of the currently available theoretical and experimental techniques to study these phenomena, including the use of trap-based positron beam sources to study collision processes with improved energy resolution. State-resolved measurements of electronic and vibrational excitation cross sections and measurement of annihilation rates in atoms and molecules as a function of incident positron energy are discussed. Where data are available, comparisons are made with analogous electron scattering cross sections. Resonance phenomena, common in electron scattering, appear to be less common in positron scattering. Possible exceptions include the sharp onsets of positron-impact electronic and vibrational excitation of selected molecules. Recent energy-resolved studies of positron annihilation in hydrocarbons containing more than a few carbon atoms provide direct evidence that vibrational Feshbach resonances underpin the anomalously large annihilation rates observed for many polyatomic species. We discuss open questions regarding this process in larger molecules, as well as positron annihilation in smaller molecules where the theoretical picture is less clear. (topical review)

Theoretical study on magnetism induced by H vacancy in isolated Alq3 and Gaq3 molecules

Science.gov (United States)

Ju, Lin; Xu, Tongshuai; Zhang, Yongjia; Sun, Li

2017-10-01

The magnetism induced by H vacancy in isolated Alq3 and Gaq3 molecules has been studied based on density functional theory. The isolated stoichiometric Alq3 and Gaq3 molecules are non-magnetic. With an H vacancy, both Alq3 and Gaq3 molecules could show magnetism, which are mainly due to the polarization of the C 2p electrons and the magnetic moments are mainly distributed at most nearby C atoms of H vacancies. This is because the unpaired electron on the C atom appears, when the H atom nearby is removed. Six cases of the H vacancy introduced in the Alq3 and Gaq3 molecules are considered, respectively. By comparing the relative defect formation energy, the V H3 vacancy is most likely to appear in the two kinds of molecules. In addition, for the ground state configuration of isolated Alq3 and Gaq3 molecules with two H vacancies, the energy of the ferromagnetic state is lower than that of the antiferromagnetic state, which means that the ferromagnetic state is stable. The ferromagnetic mechanism can be explained by the Heisenberg direct exchange interaction between two the polarized C atoms. Our work opens a new way to synthesize organic magnetic materials and perfects the theory of organic ferromagnetism by introducing the d 0 ferromagnetism.

Matrix isolation sublimation: An apparatus for producing cryogenic beams of atoms and molecules

Energy Technology Data Exchange (ETDEWEB)

Sacramento, R. L.; Alves, B. X.; Silva, B. A.; Wolff, W.; Cesar, C. L. [Instituto de Física, Universidade Federal do Rio de Janeiro, Caixa Postal 68528, 21941-972 Rio de Janeiro, RJ (Brazil); Oliveira, A. N. [Instituto de Física, Universidade Federal do Rio de Janeiro, Caixa Postal 68528, 21941-972 Rio de Janeiro, RJ (Brazil); INMETRO, Av. Nossa Senhora das Graças, 50 25250-020 Duque de Caxias, RJ (Brazil); Li, M. S. [Instituto de Física de São Carlos, Universidade de São Paulo, Ave. Trabalhador São Carlense, 400, 13565-590 São Carlos, SP (Brazil)

2015-07-15

We describe the apparatus to generate cryogenic beams of atoms and molecules based on matrix isolation sublimation. Isolation matrices of Ne and H{sub 2} are hosts for atomic and molecular species which are sublimated into vacuum at cryogenic temperatures. The resulting cryogenic beams are used for high-resolution laser spectroscopy. The technique also aims at loading atomic and molecular traps.

Investigation of N-acyl homoserine lactone (AHL) molecule production in Gram-negative bacteria isolated from cooling tower water and biofilm samples.

Science.gov (United States)

Haslan, Ezgi; Kimiran-Erdem, Ayten

2013-09-01

In this study, 99 Gram-negative rod bacteria were isolated from cooling tower water, and biofilm samples were examined for cell-to-cell signaling systems, N-acyl homoserine lactone (AHL) signal molecule types, and biofilm formation capacity. Four of 39 (10 %) strains isolated from water samples and 14 of 60 (23 %) strains isolated from biofilm samples were found to be producing a variety of AHL signal molecules. It was determined that the AHL signal molecule production ability and the biofilm formation capacity of sessile bacteria is higher than planktonic bacteria, and there was a statistically significant difference between the AHL signal molecule production of these two groups (p cooling tower water and biofilm samples produced different types of AHL signal molecules and that there were different types of AHL signal molecules in an AHL extract of bacteria. In the present study, it was observed that different isolates of the same strains did not produce the same AHLs or did not produce AHL molecules, and bacteria known as AHL producers did not produce AHL. These findings suggest that detection of signal molecules in bacteria isolated from cooling towers may contribute to prevention of biofilm formation, elimination of communication among bacteria in water systems, and blockage of quorum-sensing controlled virulence of these bacteria.

Mixed Quantum/Classical Theory for Molecule-Molecule Inelastic Scattering: Derivations of Equations and Application to N2 + H2 System.

Science.gov (United States)

Semenov, Alexander; Babikov, Dmitri

2015-12-17

The mixed quantum classical theory, MQCT, for inelastic scattering of two molecules is developed, in which the internal (rotational, vibrational) motion of both collision partners is treated with quantum mechanics, and the molecule-molecule scattering (translational motion) is described by classical trajectories. The resultant MQCT formalism includes a system of coupled differential equations for quantum probability amplitudes, and the classical equations of motion in the mean-field potential. Numerical tests of this theory are carried out for several most important rotational state-to-state transitions in the N2 + H2 system, in a broad range of collision energies. Besides scattering resonances (at low collision energies) excellent agreement with full-quantum results is obtained, including the excitation thresholds, the maxima of cross sections, and even some smaller features, such as slight oscillations of energy dependencies. Most importantly, at higher energies the results of MQCT are nearly identical to the full quantum results, which makes this approach a good alternative to the full-quantum calculations that become computationally expensive at higher collision energies and for heavier collision partners. Extensions of this theory to include vibrational transitions or general asymmetric-top rotor (polyatomic) molecules are relatively straightforward.

Can Internal Conversion BE Controlled by Mode-Specific Vibrational Excitation in Polyatomic Molecules

Science.gov (United States)

Portnov, Alexander; Epshtein, Michael; Bar, Ilana

2017-06-01

Nonadiabatic processes, dominated by dynamic passage of reactive fluxes through conical intersections (CIs) are considered to be appealing means for manipulating reaction paths. One approach that is considered to be effective in controlling the course of dissociation processes is the selective excitation of vibrational modes containing a considerable component of motion. Here, we have chosen to study the predissociation of the model test molecule, methylamine and its deuterated isotopologues, excited to well-characterized quantum states on the first excited electronic state, S_{1}, by following the N-H(D) bond fission dynamics through sensitive H(D) photofragment probing. The branching ratios between slow and fast H(D) photofragments, the internal energies of their counter radical photofragments and the anisotropy parameters for fast H photofragments, confirm correlated anomalies for predissociation initiated from specific rovibronic states, reflecting the existence of a dynamic resonance in each molecule. This resonance strongly depends on the energy of the initially excited rovibronic states, the evolving vibrational mode on the repulsive S_{1} part during N-H(D) bond elongation, and the manipulated passage through the CI that leads to radicals excited with C-N-H(D) bending and preferential perpendicular bond breaking, relative to the photolyzing laser polarization, in molecules containing the NH_{2} group. The indicated resonance plays an important role in the bifurcation dynamics at the CI and can be foreseen to exist in other photoinitiated processes and to control their outcome.

An exactly solvable model for multiphoton excitation of polyatomic molecules in the presence of collisions

International Nuclear Information System (INIS)

Strekalov, M L

2013-01-01

A theoretical study has been made on the non-stationary phenomena in the relaxation of highly vibrationally excited molecules under laser radiation giving rise to these molecules. An exact analytical solution to the master equation has been obtained in terms of Meixner polynomials with regard to VV and VT processes. The time-dependent vibrational distribution is used to obtain analytical expressions for the mean number of photons, stored on the vibrational degrees of freedom and transferred to a thermal bath. Using the latter result, an explicit expression is given for the average energy transfer as a function of time. Its dependence on the partial pressure of absorbing molecules has also been established. (paper)

Isolation and Characterisation of Some Microalgae Bioactive Molecules

Directory of Open Access Journals (Sweden)

Emeka Ugoala

2016-12-01

Full Text Available This study involved the isolation, structure elucidation, and biological screening of secondary metabolites in freshwater microalgae for bioactive and chemically novel compounds. Isolates were fractionated and purified from the methanol, ethyl acetate, dichloromethane, petroleum ether and aqueous extracts of microalgae via column chromatography technique over silica gel using a gradient mixture of solvents. The chemical structures of isolated compounds have been elucidated using Solid-state cross polarization (CP and magic angle spinning (MAS 13C-NMR spectroscopic technique at spectrometer frequency at a field strength corresponding to 91.3695 MHz for 13C and 363.331 MHz for 1H. Of the nine compounds isolated, eight have a glycan skeleton with attached amino acids units. Two of the eight contain beta amino acids units. These are not very common metabolites but hold promise as drug leads. The elements of diversity in the isolates were the gluco and manno configurations of the pyranose ring, the α-configurations at the anomeric centre, and the positions of the carbohydrate and amino acid sectors in the ring. These molecules are not easily available through gene technology since they are post translational products resulting from the activity of glycosyl hydrolases and transferases. The chemical shifts were rationalized in terms of the number of sugar residues, the sugar ring structures, the positions and anomeric configurations of the inter-sugar linkages. Considering all the NMR data, it was concluded that the compounds were glycylglycylglycylglycine, α-D-glucopyranosyl-2-amino-4-methylpentanoic acid, α-D-glucopyranosyl-2-methylamino-4-methylpentanoic acid, α-D-glucopyranosyl-2-amino-4-methylpentanoate, α-D-glucopyranosyl-glycylglycine, α-D-glucopyranosyl-3-aminobutanoic acid, α-D-glucopyranosyl-2,4,7-triaminooctantrioic acid, α-D-mannopyranosyl-2-amino-3-methylbutanoic acid and α-D-mannopyranosyl-3-aminobutanoic acid.

Diffractive Imaging of Coherent Nuclear Motion in Isolated Molecules

Energy Technology Data Exchange (ETDEWEB)

Yang, Jie; Guehr, Markus; Shen, Xiaozhe; Li, Renkai; Vecchione, Theodore; Coffee, Ryan; Corbett, Jeff; Fry, Alan; Hartmann, Nick; Hast, Carsten; Hegazy, Kareem; Jobe, Keith; Makasyuk, Igor; Robinson, Joseph; Robinson, Matthew S.; Vetter, Sharon; Weathersby, Stephen; Yoneda, Charles; Wang, Xijie; Centurion, Martin

2016-10-03

Observing the motion of the nuclear wave packets during a molecular reaction, in both space and time, is crucial for understanding and controlling the outcome of photoinduced chemical reactions. We have imaged the motion of a vibrational wave packet in isolated iodine molecules using ultrafast electron diffraction with relativistic electrons. The time-varying interatomic distance was measured with a precision 0.07 Å and temporal resolution of 230 fs full width at half maximum. The method is not only sensitive to the position but also the shape of the nuclear wave packet.

The second-order description of rotational non-equilibrium effects in polyatomic gases

Science.gov (United States)

Myong, Rho Shin

2017-11-01

The conventional description of gases is based on the physical laws of conservation (mass, momentum, and energy) in conjunction with the first-order constitutive laws, the two-century old so-called Navier-Stokes-Fourier (NSF) equation based on a critical assumption made by Stokes in 1845 that the bulk viscosity vanishes. While the Stokes' assumption is certainly legitimate in the case of dilute monatomic gases, ever increasing evidences, however, now indicate that such is not the case, in particular, in the case of polyatomic gases-like nitrogen and carbon dioxide-far-from local thermal equilibrium. It should be noted that, from room temperature acoustic attenuation data, the bulk viscosity for carbon dioxide is three orders of magnitude larger than its shear viscosity. In this study, this fundamental issue in compressible gas dynamics is revisited and the second-order constitutive laws are derived by starting from the Boltzmann-Curtiss kinetic equation. Then the topology of the second-order nonlinear coupled constitutive relations in phase space is investigated. Finally, the shock-vortex interaction problem where the strong interaction of two important thermal (translational and rotational) non-equilibrium phenomena occurs is considered in order to highlight the rotational non-equilibrium effects in polyatomic gases. This work was supported by the National Research Foundation of South Korea (NRF 2017-R1A2B2-007634).

On the trends of Fukui potential and hardness potential derivatives in isolated atoms vs. atoms in molecules.

Science.gov (United States)

Bhattacharjee, Rituparna; Roy, Ram Kinkar

2014-10-28

In the present study, trends of electronic contribution to molecular electrostatic potential [Vel(r¯)(r=0)], Fukui potential [v(+)f|(r=0) and v(-)f|(r=0)] and hardness potential derivatives [Δ(+)h(k) and Δ(-)h(k)] for isolated atoms as well as atoms in molecules are investigated. The generated numerical values of these three reactivity descriptors in these two electronically different situations are critically analyzed through the relevant formalism. Values of Vel(r¯) (when r → 0, i.e., on the nucleus) are higher for atoms in molecules than that of isolated atoms. In contrast, higher values of v(+)|(r=0) and v(-)|(r=0) are observed for isolated atoms compared to the values for atoms in a molecule. However, no such regular trend is observed for the Δ(+)h(k) and Δ(-)h(k) values, which is attributed to the uncertainty in the Fukui function values of atoms in molecules. The sum of Fukui potential and the sum of hardness potential derivatives in molecules are also critically analyzed, which shows the efficacy of orbital relaxation effects in quantifying the values of these parameters. The chemical consequence of the observed trends of these descriptors in interpreting electron delocalization, electronic relaxation and non-negativity of atomic Fukui function indices is also touched upon. Several commonly used molecules containing carbon as well as heteroatoms are chosen to make the investigation more insightful.

Laser ablation-inductively coupled plasma-mass spectrometry: Examinations of the origins of polyatomic ions and advances in the sampling of particulates

Energy Technology Data Exchange (ETDEWEB)

Witte, Travis [Iowa State Univ., Ames, IA (United States)

2011-01-01

This dissertation provides a general introduction to Inductively coupled plasma-mass spectrometry (ICP-MS) and laser ablation (LA) sampling, with an examination of analytical challenges in the employment of this technique. It discusses the origin of metal oxide ions (MO+) in LA-ICP-MS, as well as the effect of introducing helium and nitrogen to the aerosol gas flow on the formation of these polyatomic interferences. It extends the study of polyatomic ions in LA-ICP-MS to metal argide (MAr+) species, an additional source of possible significant interferences in the spectrum. It describes the application of fs-LA-ICP-MS to the determination of uranium isotope ratios in particulate samples.

Damage functions generation for polyatomic materials irradiated in test reactors

International Nuclear Information System (INIS)

Alberman, A.; Lesueur, D.

1987-06-01

Neutron exposure parameters in polyatomic materials is of great importance for fusion technology programs. The COMPOSI code computes the number of displaced atoms of sub-lattice ''j'' induced by one atom of sub-lattice ''i'' either by direct collision or through intermediate knocked atom. The code uses Lindhard equations; it is solved by iterative process. The atomic displacements cross-sections, as a function of neutron energy are derived by folding previous results with ''i'' type PKA. Moreover the COMPOSI code may include recoils from charged particles e.g.: Alpha + Triton from Li 6 capture in Li Al 0 2 . These responses in various spectra are discussed [fr

Interaction of VUV-photons with molecules. Spectroscopy and dynamics of molecular superexcited states

International Nuclear Information System (INIS)

Hatano, Y.

2002-01-01

Complete text of publication follows. A survey is given of recent progress in experimental studies of the interaction of VUV-photons with molecules, i.e., those of photoabsorption, photoionization, and photodissociation of molecules in the excitation photon energy range of 10-50 eV, with a particular emphasis placed on current understanding of the spectroscopy and dynamics of formed molecular superexcited states. These studies are of great importance in understanding the interaction of ionizing radiation with matter. Molecules studied are ranged from simple diatomic and triatomic molecules to polyatomic molecules such as hydrocarbons. Most of the observed molecular superexcited states are assigned to high Rydber states which are vibrationally, doubly, or inner-core excited and converge to each of ion states. Non-Rydberg superexcited states are also observed. Dissociation into neutral fragments in comparison with ionization is of unexpectedly great importance in the observed decay of each of these state-assigned superexcited molecules. Dissociation dynamics as well as its products of superexcited states are remarkably different from those of lower excited states below about ionization thresholds. Some remarks are also presented of molecules in the condensed phase

Quantification of ion-induced molecular fragmentation of isolated 2-deoxy-D-ribose molecules

NARCIS (Netherlands)

Alvarado Chacon, F.; Bari, S.; Hoekstra, R.A.; Schlathölter, T.A.

2006-01-01

Recent experiments on low energy ion-induced damage to DNA building blocks indicate that ion induced DNA damage is dominated by deoxyribose disintegration (Phys. Rev. Lett., 2005, 95, 153201). We have studied interactions of keV H+ and Heq+ with isolated deoxyribose molecules by means of high

Positron scattering by molecules: implementation of the C-tilde-functional; Espalhamento de positrons por moleculas: implementacao do funcional-C-tilde

Energy Technology Data Exchange (ETDEWEB)

Silva Lino, Jorge Luiz da

1995-12-31

In this work, we present a formulation called the C-Functional to study collisions of low-energy positron by molecules. This formalism is based on the Schwinger Multichannel Method for positrons which although being a quite general method (it is applicable to polyatomic molecules and include polarization and multichannel coupling) is limited to the use of trial wavefunctions consisting only of square integrable basis functions (Gaussian Cartesian Function). In principle this is not a problem, considering that the Schwinger type of methods require a good description of the scattering wavefunction only in the region where the potential is non-zero. However, there exist some situations (long range potentials) where the SMC has consequences. The C-functional (CF) consists in writing the wavefunctions as a sum of a plane-wave plus a combination of trial functions (where the combination is variationally determined). The basic difference between the 2 cases (SMC and CF) is the presence in the CF amplitude of the First (FBA) and Second Born terms. Aiming the preservation of important features of the SMG, we have developed general codes (applicable to polyatomic targets) to evaluate these terms. To illustrate the CF method we show elastic cross sections ti He and H{sub 2}. (author) 36 refs., 46 figs., 19 tabs.

Photodissociation dynamics of polyatomic molecules

Energy Technology Data Exchange (ETDEWEB)

Zhao, Hequan [Iowa State Univ., Ames, IA (United States)

1998-02-23

This report consists of five studies as follows: A laser photofragmentation time-of-flight mass spectrometric study of acetophenone at 193 and 248 nm; A 193 nm laser photofragmentation time-of-flight mass spectrometric study of dimethylsulfoxide; 193 nm laser photofragmentation time-of-flight mass spectrometric study of HSCH₂CH₂SH; Thiophene biradical decay of the primary laser photofragmentation product at 193 nm; and Scattering cross sections for O(³P)[SO(X,³Σ^-)] + He[Ne, Ar, Kr]. Chapters are included for the introduction and general conclusions.

Hydrodynamic limits of kinetic equations for polyatomic and reactive gases

Directory of Open Access Journals (Sweden)

Bisi M.

2017-03-01

Full Text Available Starting from a kinetic BGK-model for a rarefied polyatomic gas, based on a molecular structure of discrete internal energy levels, an asymptotic Chapman-Enskog procedure is developed in the asymptotic continuum limit in order to derive consistent fluid-dynamic equations for macroscopic fields at Navier-Stokes level. In this way, the model allows to treat the gas as a mixture of mono-atomic species. Explicit expressions are given not only for dynamical pressure, but also for shear stress, diffusion velocities, and heat flux. The analysis is shown to deal properly also with a mixture of reactive gases, endowed for simplicity with translational degrees of freedom only, in which frame analogous results can be achieved.

Rotational partition functions for linear molecules

International Nuclear Information System (INIS)

McDowell, R.S.

1988-01-01

An accurate closed-form expression for the rotational partition function of linear polyatomic molecules in 1 summation electronic states is derived, including the effect of nuclear spin (significant at very low temperatures) and of quartic and sextic centrifugal distortion terms (significant at moderate and high temperatures). The proper first-order quantum correction to the classical rigid-rotator partition function is shown to yield Q/sub r/ ≅β -1 exp(β/3), where βequivalenthcB/kT and B is the rotational constant in cm -1 ; for β≥0.2 additional power-series terms in β are necessary. Comparison between the results of this treatment and exact summations are made for HCN and C 2 H 2 at temperatures from 2 to 5000 K, including separate evaluation of the contributions of nuclear spin and centrifugal distortion

Investigations into the origins of polyatomic ions in inductively coupled plasma-mass spectrometry

Energy Technology Data Exchange (ETDEWEB)

McIntyre, Sally M. [Iowa State Univ., Ames, IA (United States)

2010-01-01

An inductively coupled plasma-mass spectrometer (ICP-MS) is an elemental analytical instrument capable of determining nearly all elements in the periodic table at limits of detection in the parts per quadrillion and with a linear analytical range over 8-10 orders of magnitude. Three concentric quartz tubes make up the plasma torch. Argon gas is spiraled through the outer tube and generates the plasma powered by a looped load coil operating at 27.1 or 40.6 MHz. The argon flow of the middle channel is used to keep the plasma above the innermost tube through which solid or aqueous sample is carried in a third argon stream. A sample is progressively desolvated, atomized and ionized. The torch is operated at atmospheric pressure. To reach the reduced pressures of mass spectrometers, ions are extracted through a series of two, approximately one millimeter wide, circular apertures set in water cooled metal cones. The space between the cones is evacuated to approximately one torr. The space behind the second cone is pumped down to, or near to, the pressure needed for the mass spectrometer (MS). The first cone, called the sampler, is placed directly in the plasma plume and its position is adjusted to the point where atomic ions are most abundant. The hot plasma gas expands through the sampler orifice and in this expansion is placed the second cone, called the skimmer. After the skimmer traditional MS designs are employed, i.e. quadrupoles, magnetic sectors, time-of-flight. ICP-MS is the leading trace element analysis technique. One of its weaknesses are polyatomic ions. This dissertation has added to the fundamental understanding of some of these polyatomic ions, their origins and behavior. Although mainly continuing the work of others, certain novel approaches have been introduced here. Chapter 2 includes the first reported efforts to include high temperature corrections to the partition functions of the polyatomic ions in ICP-MS. This and other objections to preceeding

Interrogating the vibrational relaxation of highly excited polyatomics with time-resolved diode laser spectroscopy: C6H6, C6D6, and C6F6+CO2

International Nuclear Information System (INIS)

Sedlacek, A.J.; Weston, R.E. Jr.; Flynn, G.W.

1991-01-01

The vibrational relaxation of highly excited ground state benzene, benzene d 6 , and hexafluorobenzene by CO 2 has been investigated with high resolution diode laser spectroscopy. The vibrationally hot polyatomics are formed by single photon 248 nm excitation to the S 1 state followed by rapid radiationless transitions. It has been found that in all cases less than 1% of the energy initially present in the polyatomics is deposited into the high frequency mode of CO 2 (ν 3 ). An investigation of the CO 2 (00 0 1) nascent rotational distribution under single collision conditions reveals that very little rotational excitation accompanies vibrational energy transfer to the ν 3 mode. The CO 2 (ν 3 ) rotational states can be described by temperatures, T rot , as follows: C 6 H 6 , T rot =360±30 K; C 6 D 6 , T rot =350±35 K and C 6 F 6 , T rot =340±23 K. An estimate of left-angle ΔE right-angle ν3 , the mean energy transferred to the CO 2 ν 3 mode per collision, suggests that as the availability of low frequency modes in the excited molecule increases, less energy is deposited into the high frequency mode of CO 2 . Finally, evidence is presented suggesting that even at moderate laser fluences, the two-photon ionization of benzene can lead to substantial CO 2 ν 3 excitation via electron+CO 2 inelastic collisions

The T-cell accessory molecule CD4 recognizes a monomorphic determinant on isolated Ia

DEFF Research Database (Denmark)

Gay, D; Buus, S; Pasternak, J

1988-01-01

The membrane protein CD4 is commonly found on mature T cells specific for antigen in association with class II major histocompatibility complex (MHC; Ia) proteins. This correlation has led to the suggestion that CD4 binds to a monomorphic region of the Ia molecule on the antigen-presenting cell...... proteins into a planar membrane system, we show that different Ia molecules can greatly enhance the ability of a CD4+ but not a CD4- variant of this class I-restricted T hybrid to respond to isolated class I molecules. T-cell responses can be strongly augmented by the concurrent expression of CD4 on the T...... cell and any of four different Ia proteins on planar membranes, thus supporting the idea that CD4 binds to a monomorphic region of the Ia molecule and increases the avidity with which the T cell can interact with its target....

Contribution to the understanding of ion-gas reactions in ICP-MS collision reaction cells: application to the resolution of isobaric and polyatomic interferences

International Nuclear Information System (INIS)

Quemet, A.

2012-01-01

Inductively Coupled Plasma Mass Spectrometry (ICP-MS) emerged as the most essential technique in inorganic analytical chemistry thanks to its numerous assets, particularly its flexibility, its sensitivity and its reproducibility. As part of the elementary and isotopic analysis of irradiated fuel and transmutation target, the analyst is faced with a complex mass spectrum, due to the presence of many radionuclides. ICP-MS can not differentiate ions with the same mass, which induces isobaric and polyatomic interferences when the ions at the same mass are different chemical species. Last generations of ICP-MS have introduced collision reaction cells. It can in situ reduce these isobaric or polyatomic interferences. The cell is a multipole (quadrupole, hexapole or octupole) device filled with a collision and/or reaction gas. The gas molecules collide or possibly react with the ion beam, which eliminates or reduces interferences. Such resolution of interferences is based on the difference of chemical behaviours between the analyte and the interfering species: the choice of the gas is crucial. A better understanding of the 'ion - gas' reaction should help choosing the reacting gases. Three ICP-MS, with the different cell geometries, were used for this study: Perkin Elmer Elan DRC e (quadrupole), Thermo Fischer X serie II (hexapole) and Agilent Technologies 7700x (octupole). The effects of the cell geometry on different experimental parameters and on the resolution of the 56 Fe + / 40 Ar 16 O + polyatomic interferences were examined to measure iron at trace or ultra-trace level. This preliminary study was applied to measure iron as impurities in uranium oxide, the method was then validated with a Certified Reference Material. The reactivities of transition metals (Zr, Ru, Pd, Ag, Cd, Sn), lanthanides (La, Ce, Nd, Sm, Eu, Gd, Dy, Er and Yb) and actinides (U, Np, Pu, Am and Cm), elements of interest in the nuclear field, are studied with numerous gases (O 2 , CO, CO 2 , N 2

Strong-field ionization of linear molecules by a bicircular laser field: Symmetry considerations

Science.gov (United States)

Gazibegović-Busuladžić, A.; Busuladžić, M.; Hasović, E.; Becker, W.; Milošević, D. B.

2018-04-01

Using the improved molecular strong-field approximation, we investigate (high-order) above-threshold ionization [(H)ATI] of various linear polyatomic molecules by a two-color laser field of frequencies r ω and s ω (with integer numbers r and s ) having coplanar counter-rotating circularly polarized components (a so-called bicircular field). Reflection and rotational symmetries for molecules aligned in the laser-field polarization plane, analyzed for diatomic homonuclear molecules in Phys. Rev. A 95, 033411 (2017), 10.1103/PhysRevA.95.033411, are now considered for diatomic heteronuclear molecules and symmetric and asymmetric linear triatomic molecules. There are additional rotational symmetries for (H)ATI spectra of symmetric linear molecules compared to (H)ATI spectra of the asymmetric ones. It is shown that these symmetries manifest themselves differently for r +s odd and r +s even. For example, HATI spectra for symmetric molecules with r +s even obey inversion symmetry. For ATI spectra of linear molecules, reflection symmetry appears only for certain molecular orientation angles ±90∘-j r 180∘/(r +s ) (j integer). For symmetric linear molecules, reflection symmetry appears also for the angles -j r 180∘/(r +s ) . For perpendicular orientation of molecules with respect to the laser-field polarization plane, the HATI spectra are very similar to those of the atomic targets, i.e., both spectra are characterized by the same type of the (r +s )-fold symmetry.

Low energy elastic electron scattering from polyatomic targets

International Nuclear Information System (INIS)

Khakoo, M A

2008-01-01

New differential cross-section measurements for elastic electron scattering from ethylene (C 2 H 4 ), three primary alcohols, methanol (CH 3 OH), ethanol (C 2 H 5 OH) and propanol (C 3 H 7 OH) are reported. The measurements are obtained using the relative flow method with a thin aperture as the collimating target gas source. The relative flow method is applied without the molecular diameters restriction imposed by the relative flow pressure condition on helium (the calibrating gas) and the unknown gases (the primary alcohols). The experimental data were taken at incident electron energies of 1eV, 2eV, 5eV, 10eV, 15eV, 20eV, 30eV, 50eV and 100eV, but only a brief survey of these results will be made here. The experimental results are compared to theoretical differential cross-sections are obtained by using the variational multi-channel Schwinger method. Initial comparisons between theory and experiment show that present theory is well-able to model low electron scattering from these polyatomic targets.

Rational extended thermodynamics of a rarefied polyatomic gas with molecular relaxation processes

Science.gov (United States)

Arima, Takashi; Ruggeri, Tommaso; Sugiyama, Masaru

2017-10-01

We present a more refined version of rational extended thermodynamics of rarefied polyatomic gases in which molecular rotational and vibrational relaxation processes are treated individually. In this case, we need a triple hierarchy of the moment system and the system of balance equations is closed via the maximum entropy principle. Three different types of the production terms in the system, which are suggested by a generalized BGK-type collision term in the Boltzmann equation, are adopted. In particular, the rational extended thermodynamic theory with seven independent fields (ET7) is analyzed in detail. Finally, the dispersion relation of ultrasonic wave derived from the ET7 theory is confirmed by the experimental data for CO2, Cl2, and Br2 gases.

Calculations on isotope separation by laser induced photodissociation of polyatomic molecules. Progress report, February 1, 1977--June 30, 1978

International Nuclear Information System (INIS)

Lamb, W.E. Jr.

1978-07-01

The molecule SF 6 is treated as a classical dynamical system obeying Newton's laws of motion. This report describes how the current SF 6 potential is determined. The initial approach is described in terms of a pair of Lennard--Jones potential functions with arbitrary coefficients. A method for determining the potential constants is developed. The SF 6 spectrum was reproduced by including three-body forces. By specifying certain parameters such as the 1/r 6 F-F constant and the total dissociation energy of the molecule, a satisfactory global potential was obtained. The laser-molecule interaction energy was developed

Comparison of two screening corrections to the additivity rule for the calculation of electron scattering from polyatomic molecules

International Nuclear Information System (INIS)

Blanco, F.; Rosado, J.; Illana, A.; Garcia, G.

2010-01-01

The SCAR and EGAR procedures have been proposed in order to extend to lower energies the applicability of the additivity rule for calculation of electron-molecule total cross sections. Both those approximate treatments arise after considering geometrical screening corrections due to partial overlapping of atoms in the molecule, as seen by the incident electrons. The main features, results and limitations of both treatments are put here in comparison by means of their application to some different sized species.

A BGK model for reactive mixtures of polyatomic gases with continuous internal energy

Science.gov (United States)

Bisi, M.; Monaco, R.; Soares, A. J.

2018-03-01

In this paper we derive a BGK relaxation model for a mixture of polyatomic gases with a continuous structure of internal energies. The emphasis of the paper is on the case of a quaternary mixture undergoing a reversible chemical reaction of bimolecular type. For such a mixture we prove an H -theorem and characterize the equilibrium solutions with the related mass action law of chemical kinetics. Further, a Chapman-Enskog asymptotic analysis is performed in view of computing the first-order non-equilibrium corrections to the distribution functions and investigating the transport properties of the reactive mixture. The chemical reaction rate is explicitly derived at the first order and the balance equations for the constituent number densities are derived at the Euler level.

Ion beam studies - part 4. The use of multiply-charged and polyatomic ions in an implantation accelerator

International Nuclear Information System (INIS)

Freeman, J.H.; Chivers, D.J.; Gard, G.A.

1976-12-01

Polyatomic and multiply-charged ion provide a convenient means of extending the energy range of an implanted accelerator. The molecular species are also of interest in certain special bombardment studies. This report considers some of the factors which affect the production and utilisation of such beams. It introduces the concepts of hetero- and auto-contamination, and particular attention is given to the modification of the charge or mass of the ions resulting from inelastic collisions in the various beams transport regions of the accelerator. (author)

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

International Nuclear Information System (INIS)

Chu, P.M.Y.

1991-10-01

The vibrational to translational (V→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→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 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

Laser fluorimetry of mixtures of polyatomic organic compounds using artificial neural networks

International Nuclear Information System (INIS)

Dolenko, S A; Gerdova, I V; Dolenko, T A; Fadeev, V V

2001-01-01

New possibilities of laser fluorimetry offered by the use of algorithms for solving inverse problems based on artificial neural networks are demonstrated. A two-component mixture of polyatomic organic compounds is analysed by three methods of laser fluorimetry: a direct analysis of the fluorescence band, the kinetic fluorimetry (when durations of the laser pulse and the detector gate pulse are comparable with the fluorescence lifetimes or exceed them), and the saturation fluorimetry. The numerical experiments showed that the use of artificial neural networks in these methods provides a high practical stability of the solution of inverse problems and ensures a high sensitivity and a high accuracy of determining the contribution of components to fluorescence and of measuring molecular photophysical parameters, which can be used for the identification of components. (laser applications and other topics in quantum electronics)

Isolated single-molecule magnets on native gold.

Science.gov (United States)

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

2005-03-28

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

Application of the generator coordinates method to the intra-molecular proton tunneling in the malonaldehyde molecule

International Nuclear Information System (INIS)

Schmidt, Andre Campos Kersten

1995-01-01

The effects of different vibrational modes on the isomerization process of polyatomic molecules, or solvent's effects on reaction rates are object of up-to-date interest. In general, such many body phenomena are, in principle, multidimensional, and they first require a reduction of relevant degrees of freedom. In order to investigated, some aspects of the intra-molecular proton tunneling on a malonaldehyde molecule, we use the Generator Coordinate Method. The model used to describe such a process is the so-called System-Bath model, where the system is the reaction coordinate and the bath are the intrinsic degrees of freedom (vibrational modes of the molecule), which are described by a harmonic oscillator set linearly coupled to the system. The reduction of the multidimensional problem to the effective unidimensional one is done using a energy related variational principle on the intrinsic degrees of freedom. we obtained analytically a effective Hamiltonian where the effects of the various degrees of freedom reveal themselves in the appearance of a effective mass and in changes of the shape of the potential barrier. The analyticity of the method was crucial on identifying clearly the roles played by the different physical parameters involved. (author)

Path-integral approach to resonant electron-molecule scattering

International Nuclear Information System (INIS)

Winterstetter, M.; Domcke, W.

1993-01-01

A path-integral formulation of resonant electron-molecule scattering is developed within the framework of the projection-operator formalism of scattering theory. The formation and decay of resonances is treated in real time as a quantum-mechanical electronic-tunneling process, modified by the coupling of the electronic motion with the nuclear degrees of freedom. It is shown that the electronic continuum can be summed over in the path-integral formulation, resulting formally in the path integral for an effective two-state system with coupling to vibrations. The harmonic-oscillator approximation is adopted for the vibrational motion in the present work. Approximation methods are introduced which render the numerical evaluation of the sum over paths feasible for up to ∼10 3 elementary time slices. The theory is numerically realized for simple but nontrivial models representing the 2 Π g d-wave shape resonance in e - +N 2 collisions and the 2 Σ u + p-wave shape resonance in e - +H 2 collisions, respectively. The accuracy of the path-integral results is assessed by comparison with exact numerical reference data for these models. The essential virtue of the path-integral approach is the fact that the computational effort scales at most linearly with the number of vibrational degrees of freedom. The path-integral method is thus well suited to treat electron collisions with polyatomic molecules and molecular aggregates

Isolation and Purification of an Early Pregnancy Factor–Like Molecule from Culture Supernatants Obtained from Lymphocytes of Pregnant Women

OpenAIRE

Aranha, Clara; Natraj, Usha; Iyer, K. S.; Shahani, Savitri

1998-01-01

Purpose:Our purpose was to determine whether lymphocytes synthesize proteins during pregnancy, to observe whether one of the proteins synthesized has early pregnancy factor (EPF)–like activity and to isolate and purify this molecule from culture supernatants obtained from stimulated lymphocytes of pregnant women.

How to determine the handedness of single molecules using Coulomb explosion imaging

International Nuclear Information System (INIS)

Pitzer, Martin

2017-01-01

This tutorial is based on a doctoral thesis that was shortlisted for the 2016 AMOP dissertation prize of the German Physical Society (DPG). The principal achievement of the thesis was to use Coulomb explosion imaging (CEI) to determine the microscopic handedness (‘chirality’) of molecular structures on a single-molecule level. It thus shows how a technique developed in atomic physics can address a long-standing problem in chemistry. Owing to these disparate backgrounds, the tutorial has two facets: on the one hand, the history of molecular chirality and recent developments are very briefly reviewed. On the other hand, an account is given of different experimental approaches to CEI, on the physical processes in light-induced Coulomb explosion and—most importantly—on the aspects that are relevant when designing and performing such an experiment. As structural chirality occurs only in polyatomic molecules, special attention will be given to multiple ionization and multi-coincidence measurements. A short discussion of the results presented in earlier papers is given, followed by an outlook on experiments that are under way or can realistically be performed within the next years. (phd tutorial)

Three methods to measure RH bond energies

International Nuclear Information System (INIS)

Berkowitz, J.; Ellison, G.B.; Gutman, D.

1993-01-01

In this paper the authors compare and contrast three powerful methods for experimentally measuring bond energies in polyatomic molecules. The methods are: radical kinetics; gas phase acidity cycles; and photoionization mass spectroscopy. The knowledge of the values of bond energies are a basic piece of information to a chemist. Chemical reactions involve the making and breaking of chemical bonds. It has been shown that comparable bonds in polyatomic molecules, compared to the same bonds in radicals, can be significantly different. These bond energies can be measured in terms of bond dissociation energies

Using polyatomic primary ions to probe an amino acid and a nucleic base in water ice

Energy Technology Data Exchange (ETDEWEB)

Conlan, X.A. [Surface Analysis Research Centre, School of Chemical Engineering and Analytical Science, University of Manchester, P.O. Box 88, Manchester M60 1QD (United Kingdom)]. E-mail: x.conlan@postgrad.manchester.ac.uk; Biddulph, G.X. [Surface Analysis Research Centre, School of Chemical Engineering and Analytical Science, University of Manchester, P.O. Box 88, Manchester M60 1QD (United Kingdom)]. E-mail: G.Biddulph@postgrad.manchester.ac.uk; Lockyer, N.P. [Surface Analysis Research Centre, School of Chemical Engineering and Analytical Science, University of Manchester, P.O. Box 88, Manchester M60 1QD (United Kingdom); Vickerman, J.C. [Surface Analysis Research Centre, School of Chemical Engineering and Analytical Science, University of Manchester, P.O. Box 88, Manchester M60 1QD (United Kingdom)]. E-mail: John.Vickerman@manchester.ac.uk

2006-07-30

In this study on pure water ice, we show that protonated water species [H{sub 2}O] {sub n}H{sup +} are more prevalent than (H{sub 2}O) {sub n} {sup +} ions after bombardment by Au{sup +} monoatomic and Au{sub 3} {sup +} and C{sub 60} {sup +} polyatomic projectiles. This data also reveals significant differences in water cluster yields under bombardment by these three projectiles. The amino acid alanine and the nucleic base adenine in solution have been studied and have been shown to have an effect on the water cluster ion yields observed using an Au{sub 3} {sup +} ion beam.

Multiphoton processes in isolated atoms and molecules

International Nuclear Information System (INIS)

Sudbo, A.S.

1979-11-01

The theory of coherent excitation of a multilevel quantum mechanical system is developed. Damping of the system is taken into account by the use of a density matrix formalism. General properties of the wave function and/or the density matrix are discussed. The physical implications for the behavior of the system are described, together with possible applications of the formalism, including the infrared multiphoton excitation of molecules, and optical pumping in alkali atoms. Experimental results are presented on the infrared multiphoton dissociation of molecules, followed by a discussion of the general features of this process. The experimental results were obtained using a crossed laser and molecular beam method, and the emphasis is on determining the properties of the dissociating molecule and the dissociation products. The dissociation process is shown to be described very well by the standard statistical theory (RRKM theory) of unimolecular reactions, a brief presentation of which is also included

High resolution studies of the origins of polyatomic ions in inductively coupled plasma-mass spectrometry, Part I. Identification methods and effects of neutral gas density assumptions, extraction voltage, and cone material

International Nuclear Information System (INIS)

Ferguson, Jill Wisnewski; Houk, R.S.

2006-01-01

Common polyatomic ions (ArO + , NO + , H 2 O + , H 3 O + , Ar 2 + , ArN + , OH + , ArH + , O 2 + ) in inductively coupled plasma-mass spectrometry (ICP-MS) are identified using high mass resolution and studied using kinetic gas temperatures (T gas ) determined from a dissociation reaction approach. Methods for making accurate mass measurements, confirming ion identifications, and correcting for mass bias are discussed. The effects of sampler and skimmer cone composition and extraction voltage on polyatomic ion formation are also explored. Neutral species densities at several locations in the extraction interface are estimated and the corresponding effects of the T gas value are calculated. The results provide information about the origins of background ions and indicate possible locations for their formation or removal

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

International Nuclear Information System (INIS)

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

2012-01-01

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 (CH 3 OCH 2 COCH 3 and CH 3 COCOCH 3 ) dissociated effectively yielding · CH 3 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(CH 3 ) 3 , but it was negligible for R=–CH 3 . The mechanisms of “hot” reactions and excess energy relaxation are discussed. - Highlights: ► Radiolysis of bifunctional organic compounds and alkynes. ► Dependence of “hot” fragmentation probability from molecular structure. ► Ions of bifunctional compounds are less stable than those of monofunctional ones. ► Alkynes are rather stable to “hot” fragmentation.

Effect of the dynamic pressure on the shock wave structure in a rarefied polyatomic gas

Energy Technology Data Exchange (ETDEWEB)

Taniguchi, Shigeru, E-mail: taniguchi@stat.nitech.ac.jp; Sugiyama, Masaru, E-mail: sugiyama@nitech.ac.jp [Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555 (Japan); Arima, Takashi, E-mail: tks@stat.nitech.ac.jp [Center for Social Contribution and Collaboration, Nagoya Institute of Technology, Nagoya 466-8555 (Japan); Ruggeri, Tommaso, E-mail: tommaso.ruggeri@unibo.it [Department of Mathematics and Research Center of Applied Mathematics (CIRAM), University of Bologna, Bologna (Italy)

2014-01-15

We study the shock wave structure in a rarefied polyatomic gas based on a simplified model of extended thermodynamics in which the dissipation is due only to the dynamic pressure. In this case the differential system is very simple because it is a variant of Euler system with a new scalar equation for the dynamic pressure [T. Arima, S. Taniguchi, T. Ruggeri, and M. Sugiyama, Phys. Lett. A 376, 2799–2803 (2012)]. It is shown that this theory is able to describe the three types of the shock wave structure observed in experiments: the nearly symmetric shock wave structure (Type A, small Mach number), the asymmetric structure (Type B, moderate Mach number), and the structure composed of thin and thick layers (Type C, large Mach number)

Laser excitation of SF6: spectroscopy and coherent pulse propagation effects

International Nuclear Information System (INIS)

Cantrell, C.D.; Makarov, A.A.; Louisell, W.H.

1978-01-01

Recent theoretical studies of coherent propagation effects in SF 6 and other polyatomic molecules are summarized beginning with an account of relevant aspects of the high-resolution spectroscopy of the ν 3 band of SF 6 . A laser pulse propagating in a molecular gas can acquire new frequencies which were not initially present in the pulse, and, in fact, a wave is coherently generated at the frequency of every molecular transition accessible from the initial molecular energy levels. The possible consequences of coherent generation of sidebands for the multiple-photon excitation of SF 6 and other polyatomic molecules are discussed

Universal imaging: Dissociative ionization of polyatomic molecules, chemical dynamics beamline 9.0.2

Energy Technology Data Exchange (ETDEWEB)

Ahmed, M.; Chen, D.; Suits, A.G. [Ernest Orlando Lawrence Berkeley National Lab., CA (United States)

1997-04-01

A third endstation was recently added to the Chemical Dynamics beamline, designed to exploit the high flux broadband undulator light for a range of studies of reactive scattering, photochemistry and photoionization processes using time-of-flight mass spectroscopy coupled with position-sensitive detection. Two molecular beam sources are fixed at right angles, with the undulator light, or laser beams, intersecting the molecular beams at 45{degrees}. To date, beamline experiments have included a study of dissociative photoionization of a variety of molecules including N{sub 2}O and SF{sub 6}. In this mode, a single molecular beam source is used, with the tunable undulator light inducing, in SF{sub 6} for example, the process SF{sub 6} {r_arrow} SF{sub 6}{sup +} + e{sup {minus}} {r_arrow} SF{sub 5}{sup +} + F + e{sup {minus}}. The SF{sub 5}{sup +} ions are accelerated up the flight tube, mass selected and detected as a function of position on a phosphor screen viewed by a CCD camera. The position directly reveals the recoil speed (or translational energy release) and angular distribution for the dissociative ionization process. Furthermore, this measurement is obtained for all recoil speeds and angles simultaneously. Such detailed angular information has not previously been obtained for dissociative ionization processes; typically ion time-of-flight profiles are deconvoluted to yield rough insight into the angular distributions. The recorded image is actually a 2-dimensional projection of the nascent 3-dimensional velocity distribution, but established tomographic techniques enable the authors to reconstruct the 3-D distribution.

Symbolic derivation of high-order Rayleigh-Schroedinger perturbation energies using computer algebra: Application to vibrational-rotational analysis of diatomic molecules

Energy Technology Data Exchange (ETDEWEB)

Herbert, John M. [Kansas State Univ., Manhattan, KS (United States). Dept. of Chemistry

1997-01-01

Rayleigh-Schroedinger perturbation theory is an effective and popular tool for describing low-lying vibrational and rotational states of molecules. This method, in conjunction with ab initio techniques for computation of electronic potential energy surfaces, can be used to calculate first-principles molecular vibrational-rotational energies to successive orders of approximation. Because of mathematical complexities, however, such perturbation calculations are rarely extended beyond the second order of approximation, although recent work by Herbert has provided a formula for the nth-order energy correction. This report extends that work and furnishes the remaining theoretical details (including a general formula for the Rayleigh-Schroedinger expansion coefficients) necessary for calculation of energy corrections to arbitrary order. The commercial computer algebra software Mathematica is employed to perform the prohibitively tedious symbolic manipulations necessary for derivation of generalized energy formulae in terms of universal constants, molecular constants, and quantum numbers. As a pedagogical example, a Hamiltonian operator tailored specifically to diatomic molecules is derived, and the perturbation formulae obtained from this Hamiltonian are evaluated for a number of such molecules. This work provides a foundation for future analyses of polyatomic molecules, since it demonstrates that arbitrary-order perturbation theory can successfully be applied with the aid of commercially available computer algebra software.

Optical Control of Internal Conversion in Pyrazine

Science.gov (United States)

Barry, Grant; Singha, Sima; Hu, Zhan; Seideman, Tamar; Gordon, Robert

2014-03-01

We apply quantum control schemes previously reserved for atoms and small molecules to more complex polyatomic molecules. Pyrazine was chosen as a model polyatomic molecule for its well-studied conical intersection seam between the S1 and S2 potential energy surfaces (PESs). Using shaped ultraviolet femtosecond laser pulses, we demonstrate optical control of the excited state dynamics of this molecule under collisionless conditions. This was achieved in a pump-probe experiment by employing a genetic algorithm programmed to suppress ionization of the pyrazine molecules at a preselected time. Our findings indicate that the optimized pulses localize the wave packet for times up to 1.5 ps at a location on the coupled S1/S2 PESs where ionization is energetically forbidden. Our approach is general and does not require knowledge of the molecular Hamiltonian. Funding provided by National Science Foundation grant no. CHE-0848198.

Molecule-by-Molecule Writing Using a Focused Electron Beam

DEFF Research Database (Denmark)

Van Dorp, Willem F.; Zhang, Xiaoyan; Feringa, Ben L.

2012-01-01

atoms also be written with an electron beam? We verify this with focused electron-beam-induced deposition (FEBID), a direct-write technique that has the current record for the smallest feature written by (electron) optical lithography. We show that the deposition of an organometallic precursor...... on graphene can be followed molecule-by-molecule with FEBID. The results show that mechanisms that are inherent to the process inhibit a further increase in control over the process. Hence, our results present the resolution limit of (electron) optical lithography techniques. The writing of isolated...

Numerical-analytic implementation of the higher-order canonical Van Vleck perturbation theory for the interpretation of medium-sized molecule vibrational spectra.

Science.gov (United States)

Krasnoshchekov, Sergey V; Isayeva, Elena V; Stepanov, Nikolay F

2012-04-12

Anharmonic vibrational states of semirigid polyatomic molecules are often studied using the second-order vibrational perturbation theory (VPT2). For efficient higher-order analysis, an approach based on the canonical Van Vleck perturbation theory (CVPT), the Watson Hamiltonian and operators of creation and annihilation of vibrational quanta is employed. This method allows analysis of the convergence of perturbation theory and solves a number of theoretical problems of VPT2, e.g., yields anharmonic constants y(ijk), z(ijkl), and allows the reliable evaluation of vibrational IR and Raman anharmonic intensities in the presence of resonances. Darling-Dennison and higher-order resonance coupling coefficients can be reliably evaluated as well. The method is illustrated on classic molecules: water and formaldehyde. A number of theoretical conclusions results, including the necessity of using sextic force field in the fourth order (CVPT4) and the nearly vanishing CVPT4 contributions for bending and wagging modes. The coefficients of perturbative Dunham-type Hamiltonians in high-orders of CVPT are found to conform to the rules of equality at different orders as earlier proven analytically for diatomic molecules. The method can serve as a good substitution of the more traditional VPT2.

Degradation of Bacterial Quorum Sensing Signaling Molecules by the Microscopic Yeast Trichosporon loubieri Isolated from Tropical Wetland Waters

Directory of Open Access Journals (Sweden)

Cheng-Siang Wong

2013-09-01

Full Text Available Proteobacteria produce N-acylhomoserine lactones as signaling molecules, which will bind to their cognate receptor and activate quorum sensing-mediated phenotypes in a population-dependent manner. Although quorum sensing signaling molecules can be degraded by bacteria or fungi, there is no reported work on the degradation of such molecules by basidiomycetous yeast. By using a minimal growth medium containing N-3-oxohexanoylhomoserine lactone as the sole source of carbon, a wetland water sample from Malaysia was enriched for microbial strains that can degrade N-acylhomoserine lactones, and consequently, a basidiomycetous yeast strain WW1C was isolated. Morphological phenotype and molecular analyses confirmed that WW1C was a strain of Trichosporon loubieri. We showed that WW1C degraded AHLs with N-acyl side chains ranging from 4 to 10 carbons in length, with or without oxo group substitutions at the C3 position. Re-lactonisation bioassays revealed that WW1C degraded AHLs via a lactonase activity. To the best of our knowledge, this is the first report of degradation of N-acyl-homoserine lactones and utilization of N-3-oxohexanoylhomoserine as carbon and nitrogen source for growth by basidiomycetous yeast from tropical wetland water; and the degradation of bacterial quorum sensing molecules by an eukaryotic yeast.

Manipulation of polyatomic molecules with the scanning tunnelling microscope at room temperature: chlorobenzene adsorption and desorption from Si(111)-(7 x 7)

International Nuclear Information System (INIS)

Sloan, P A; Palmer, R E

2006-01-01

We report the imaging of chlorobenzene molecules chemisorbed on the Si(111)-(7 x 7) surface at room temperature with the scanning tunnelling microscope, and the desorption of the molecules by the tunnelling current. Detailed voltage-dependent imaging (at positive bias) allows the elucidation of the number and orientation of all the adsorbate configurations in the 7 x 7 unit cell. At negative bias the adsorbate was observed to affect the imaging properties of neighbouring half unit cells. The threshold voltage required for desorption of the chlorobenzene molecules was invariant to small changes in the tip-state, the adsorption site (corner adatom, middle adatom, faulted or unfaulted half of the unit cell) and the kind of doping of the substrate (n or p type)

Short communication: Conservation of Streptococcus uberis adhesion molecule and the sua gene in strains of Streptococcus uberis isolated from geographically diverse areas.

Science.gov (United States)

Yuan, Ying; Dego, Oudessa Kerro; Chen, Xueyan; Abadin, Eurife; Chan, Shangfeng; Jory, Lauren; Kovacevic, Steven; Almeida, Raul A; Oliver, Stephen P

2014-12-01

The objective was to identify and sequence the sua gene (GenBank no. DQ232760; http://www.ncbi.nlm.nih.gov/genbank/) and detect Streptococcus uberis adhesion molecule (SUAM) expression by Western blot using serum from naturally S. uberis-infected cows in strains of S. uberis isolated in milk from cows with mastitis from geographically diverse areas of the world. All strains evaluated yielded a 4.4-kb sua-containing PCR fragment that was subsequently sequenced. Deduced SUAM AA sequences from those S. uberis strains evaluated shared >97% identity. The pepSUAM sequence located at the N terminus of SUAM was >99% identical among strains of S. uberis. Streptococcus uberis adhesion molecule expression was detected in all strains of S. uberis tested. These results suggest that sua is ubiquitous among strains of S. uberis isolated from diverse geographic locations and that SUAM is immunogenic. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Structure factors for tunneling ionization rates of molecules: General Hartree-Fock-based integral representation

Science.gov (United States)

Madsen, Lars Bojer; Jensen, Frank; Dnestryan, Andrey I.; Tolstikhin, Oleg I.

2017-07-01

In the leading-order approximation of the weak-field asymptotic theory (WFAT), the dependence of the tunneling ionization rate of a molecule in an electric field on its orientation with respect to the field is determined by the structure factor of the ionizing molecular orbital. The WFAT yields an expression for the structure factor in terms of a local property of the orbital in the asymptotic region. However, in general quantum chemistry approaches molecular orbitals are expanded in a Gaussian basis which does not reproduce their asymptotic behavior correctly. This hinders the application of the WFAT to polyatomic molecules, which are attracting increasing interest in strong-field physics. Recently, an integral-equation approach to the WFAT for tunneling ionization of one electron from an arbitrary potential has been developed. The structure factor is expressed in an integral form as a matrix element involving the ionizing orbital. The integral is not sensitive to the asymptotic behavior of the orbital, which resolves the difficulty mentioned above. Here, we extend the integral representation for the structure factor to many-electron systems treated within the Hartree-Fock method and show how it can be implemented on the basis of standard quantum chemistry software packages. We validate the methodology by considering noble-gas atoms and the CO molecule, for which accurate structure factors exist in the literature. We also present benchmark results for CO2 and for NH3 in the pyramidal and planar geometries.

Application of R-matrix theory to resonant reactive electron-molecule scattering: Vibrational excitation and dissociative attachment of N2 and F2

International Nuclear Information System (INIS)

Wong, C.F.; Light, J.C.

1984-01-01

Based on the R-matrix approach of Schneider et al. [J. Phys. B 12, L 365 (1979)] to reactive electron-molecule scattering, a new propagative R-matrix method (PRMM) is presented which is more appropriate for polyatomic systems. The new method should be useful in other calculations where complicated integrals need to be propagated. We also introduce an effective R-matrix model (ERMM) in which the usual resonance parameters (potential and width) can be used as input in model R-matrix calculations. The PRMM and ERMM have been applied to the electron-N 2 system and the electron-F 2 system. The results agree very well with previous calculations for both vibrationally inelastic scattering and dissociative attachment when identical potentials and parameters are used

Kinetics of elementary atom and radical reactions: Progress report

International Nuclear Information System (INIS)

Gordon, R.J.

1986-01-01

Our research program is concerned with the kinetics of elementary gas phase reactions and energy transfer involving polyatomic molecules. We report here on three ongoing projects: The reaction of oxygen atoms with hydrogen molecules, the electronic relaxation of NH radicals, and the vibrational relaxation of highly excited SF 6 molecules. 10 refs., 5 figs

Study of diamagnetism in uranyl complexes of some Schiff bases

International Nuclear Information System (INIS)

Dodwad, S.S.; Sawant, A.S.

1992-01-01

Uranyl complexes of Schiff bases obtained by condensing salicylaldehyde with aromatic amines have been isolated and characterised. The complexes have the formula M (LH) 2 (NO 3 ) 2 where M = UO 2 and LH = Schiff base. The magnetic susceptibilities of these complexes have been measured on a Gouy balance. These values have been compared with the computed ones. The percentage deviation between the observed and computed values of molar magnetic susceptibilities clearly show that they are outside experimental error and therefore significant. These deviations have been discussed in the light of VanVleck's, equation for molar susceptibility of polyatomic molecule. (author). 3 refs., 1 tab

Ion mobilities in diatomic gases: measurement versus prediction with non-specular scattering models.

Science.gov (United States)

Larriba, Carlos; Hogan, Christopher J

2013-05-16

Ion/electrical mobility measurements of nanoparticles and polyatomic ions are typically linked to particle/ion physical properties through either application of the Stokes-Millikan relationship or comparison to mobilities predicted from polyatomic models, which assume that gas molecules scatter specularly and elastically from rigid structural models. However, there is a discrepancy between these approaches; when specular, elastic scattering models (i.e., elastic-hard-sphere scattering, EHSS) are applied to polyatomic models of nanometer-scale ions with finite-sized impinging gas molecules, predictions are in substantial disagreement with the Stokes-Millikan equation. To rectify this discrepancy, we developed and tested a new approach for mobility calculations using polyatomic models in which non-specular (diffuse) and inelastic gas-molecule scattering is considered. Two distinct semiempirical models of gas-molecule scattering from particle surfaces were considered. In the first, which has been traditionally invoked in the study of aerosol nanoparticles, 91% of collisions are diffuse and thermally accommodating, and 9% are specular and elastic. In the second, all collisions are considered to be diffuse and accommodating, but the average speed of the gas molecules reemitted from a particle surface is 8% lower than the mean thermal speed at the particle temperature. Both scattering models attempt to mimic exchange between translational, vibrational, and rotational modes of energy during collision, as would be expected during collision between a nonmonoatomic gas molecule and a nonfrozen particle surface. The mobility calculation procedure was applied considering both hard-sphere potentials between gas molecules and the atoms within a particle and the long-range ion-induced dipole (polarization) potential. Predictions were compared to previous measurements in air near room temperature of multiply charged poly(ethylene glycol) (PEG) ions, which range in morphology from

Atomic and molecular physics

International Nuclear Information System (INIS)

Anderson, V.E.; Cox, J.T.; Huynh, Q.A.

1975-01-01

Topics covered include: electron attachment to SO 2 in high pressure gases; long-lived parent negative ions formed via nuclear-excited Feshbach resonances, part IV, a systematic study of NO 2 -containing benzene derivatives; threshold-electron excitation and compound-negative-ion states of aromatic hydrocarbons; linking of existing data on electron-molecule interactions in gases with those in the liquid phase; slowing down of subexcitation electrons in polyatomic gases; electron mobilities in high-pressure gases (''quasi-liquids''); measurement of the mobility of excess electrons in liquids; potential energy function of an excess electron in a nonpolar liquid; electron mobilities in gases and liquids; photophysics of aromatic hydrocarbons; synthesis of electron-molecule interactions with benzene and benzene derivatives; and spin-off of basic studies on electron attachment to, and elastic scattering from, polyatomic molecules. 14 figures, 2 tables

Reference interaction site model with hydrophobicity induced density inhomogeneity: An analytical theory to compute solvation properties of large hydrophobic solutes in the mixture of polyatomic solvent molecules

International Nuclear Information System (INIS)

Cao, Siqin; Sheong, Fu Kit; Huang, Xuhui

2015-01-01

Reference interaction site model (RISM) has recently become a popular approach in the study of thermodynamical and structural properties of the solvent around macromolecules. On the other hand, it was widely suggested that there exists water density depletion around large hydrophobic solutes (>1 nm), and this may pose a great challenge to the RISM theory. In this paper, we develop a new analytical theory, the Reference Interaction Site Model with Hydrophobicity induced density Inhomogeneity (RISM-HI), to compute solvent radial distribution function (RDF) around large hydrophobic solute in water as well as its mixture with other polyatomic organic solvents. To achieve this, we have explicitly considered the density inhomogeneity at the solute-solvent interface using the framework of the Yvon-Born-Green hierarchy, and the RISM theory is used to obtain the solute-solvent pair correlation. In order to efficiently solve the relevant equations while maintaining reasonable accuracy, we have also developed a new closure called the D2 closure. With this new theory, the solvent RDFs around a large hydrophobic particle in water and different water-acetonitrile mixtures could be computed, which agree well with the results of the molecular dynamics simulations. Furthermore, we show that our RISM-HI theory can also efficiently compute the solvation free energy of solute with a wide range of hydrophobicity in various water-acetonitrile solvent mixtures with a reasonable accuracy. We anticipate that our theory could be widely applied to compute the thermodynamic and structural properties for the solvation of hydrophobic solute

Surface-ionization field mass-spectrometry studies of nonequilibrium surface ionization

International Nuclear Information System (INIS)

Blashenkov, Nikolai M; Lavrent'ev, Gennadii Ya

2007-01-01

The ionization of polyatomic molecules on tungsten and tungsten oxide surfaces is considered for quasiequilibrium or essentially nonequilibrium conditions (in the latter case, the term nonequilibrium surface ionization is used for adsorbate ionization). Heterogeneous reactions are supposed to proceed through monomolecular decay of polyatomic molecules or fragments of multimolecular complexes. The nonequilibrium nature of these reactions is established. The dependences of the current density of disordered ions on the surface temperature, electric field strength, and ionized particle energy distribution are obtained in analytical form. Heterogeneous dissociation energies, the ionization potentials of radicals, and the magnitude of reaction departure from equilibrium are determined from experimental data, as are energy exchange times between reaction products and surfaces, the number of molecules in molecular complexes, and the number of effective degrees of freedom in molecules and complexes. In collecting the data a new technique relying on surface-ionization field mass-spectrometry was applied. (instruments and methods of investigation)

Molecular vibrations the theory of infrared and Raman vibrational spectra

CERN Document Server

Wilson, E Bright; Cross, Paul C

1980-01-01

Pedagogical classic and essential reference focuses on mathematics of detailed vibrational analyses of polyatomic molecules, advancing from application of wave mechanics to potential functions and methods of solving secular determinant.

The Identification of Complex Organic Molecules in the Interstellar Medium: Using Lasers and Matrix Isolation Spectroscopy to Simulate the Interstellar Environment

Science.gov (United States)

Stone, Bradley M.

1998-01-01

The Astrochemistry Group at NASA Ames Research Center is interested in the identification of large organic molecules in the interstellar medium Many smaller organic species (e.g. hydrocarbons, alcohols, etc.) have been previously identified by their radiofrequency signature due to molecular rotations. However, this becomes increasingly difficult to observe as the size of the molecule increases. Our group in interested in the identification of the carriers of the Diffuse Interstellar Bands (absorption features observed throughout the visible and near-infrared in the spectra of stars, due to species in the interstellar medium). Polycyclic Aromatic Hydrocarbons (PAHs) and related molecules are thought to be good candidates for these carriers. Laboratory experiments am performed at Ames to simulate the interstellar environment, and to compare spectra obtained from molecules in the laboratory to those derived astronomically. We are also interested in PAHs with respect to their possible connection to the UIR (Unidentified infrared) and ERE (Extended Red Emission) bands - emission features found to emanate from particular regions of our galaxy (e.g. Orion nebula, Red Rectangle, etc.). An old, "tried and proven spectroscopic technique, matrix isolation spectroscopy creates molecular conditions ideal for performing laboratory astrophysics.

Molecular structure studies by 3D imaging of fast ion beams

International Nuclear Information System (INIS)

Kanter, E.P.; Vager, Z.; Both, G.; Cooney, P.J.; Faibis, A.; Koenig, W.; Zabransky, B.J.; Zajfman, D.

1986-01-01

The use of the Coulomb-explosion technique combined with a radically new multi-particle detector, extremely thin film targets, and low-excitation ion source has enabled, for the first time, direct measurements of the complete stereochemistry of complex polyatomic molecular ions. We outline the methods used and present results for protonated acetylene (C 2 H 3 + ) and the methane cation (CH 4 + ) as examples. We demonstrate the techniques by which these methods can be generalized to determine directly vibrational motions in polyatomic molecules. 24 refs., 4 figs

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

International Nuclear Information System (INIS)

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

2011-01-01

Complete text of publication follows. Elucidation of high-energy reaction pathways in the condensed phase is an important issue for basic understanding of the radiation stability of complex organic molecules. As was shown previously, organic radical cations (RC) may undergo fragmentation or rearrangement in solid matrices due to excess energy. The probability of this process depends on both ionization potential (IP) of the molecule and molecular structure. In the present work we have studied the role of 'hot' ionic reaction channels for RC of some bifunctional compounds and alkynes. The effect of excess energy was simulated by matrix isolation method as described in detail earlier. The formation of fragmentation products was monitored by EPR and FTIR spectroscopy. In the present work it was shown that the RC of bifunctional compounds (CH 3 OCH 2 COCH 3 , CH 3 CO(CH 2 ) n COCH 3 , n 0/2) dissociated efficiently producing · CH 3 radicals upon irradiation in solid argon matrix at T ≤ 16 K. The probability of fragmentation decreases with decrease of excess energy by switching from Ar to Xe. It is worth noting that acetone RC does not show fragmentation under these conditions. Thus, bifunctional molecules were found to be less stable to 'hot' ionic fragmentation in low-temperature solids in comparison with simple prototype carbonyl compounds. In the case of alkynes of the R-C ≡ CH type, a noticeable yield of fragmentation products was observed when R = -C(CH 3 ) 3 , but it was negligible for R = -CH 3 . It means that the presence of triple bond stabilizes the molecular skeleton of linear alkynes toward 'hot' fragmentation, similarly as it was shown for alkenes. The mechanisms of 'hot' reactions and excess energy relaxation are discussed. This work was supported by the Russian Foundation for Basic Research (project 09-03-00848a).

Stroke Status Evoked Adhesion Molecule Genetic Alterations in Astrocytes Isolated from Stroke-Prone Spontaneously Hypertensive Rats and the Apigenin Inhibition of Their Expression

Directory of Open Access Journals (Sweden)

Kazuo Yamagata

2010-01-01

Full Text Available We examined the possibility that the expression of adhesion molecules is regulated differently in cultured astrocytes from stroke-prone spontaneously hypertensive rats (SHRSP/IZM rats than in those from Wistar Kyoto rats (WKY/IZM by tumor necrosis factor-alpha (TNF- or hypoxia and reoxygenation (H/R and the inhibitory effects of apigenin. It was found that the expression of vascular cell adhesion molecule-1 (VCAM-1 by TNF- in astrocytes isolated from SHRSP/IZM was increased compared with that in WKY/IZM. The expression of monocyte chemotactic protein-1 (MCP-1 mRNA induced by H/R in SHRSP/IZM astrocytes was increased compared with that in normal oxygen concentrations. Apigenin strongly attenuated TNF--induced VCAM-1 mRNA and protein expression and suppressed the adhesion of U937 cells and SHRSP/IZM astrocytes. These results suggest that the expression levels of adhesion molecules during H/R affect disease outcome and can drive SHRSP/IZM to stroke. It is suggested that apigenin regulates adhesion molecule expression in reactive astrocytes during ischemia.

A practical approach to temperature effects in dissociative electron attachment cross sections using local complex potential theory

International Nuclear Information System (INIS)

Sugioka, Yuji; Takayanagi, Toshiyuki

2012-01-01

Highlights: ► Dissociative electron attachment cross sections for polyatomic molecules are calculated by a simple theoretical approach. ► Temperature effects can be reasonably reproduced with the present model. ► All the degrees-of-freedom are taken into account in the present dynamics approach. -- Abstract: We propose a practical computational scheme to obtain temperature dependence of dissociative electron attachment cross sections to polyatomic molecules within a local complex potential theory formalism. First we perform quantum path-integral molecular dynamics simulations on the potential energy surface for the neutral molecule in order to sample initial nuclear configurations as well as momenta. Classical trajectories are subsequently integrated on the potential energy surface for the anionic state and survival probabilities are simultaneously calculated along the obtained trajectories. We have applied this simple scheme to dissociative electron attachment processes to H 2 O and CF 3 Cl, for which several previous studies are available from both the experimental and theoretical sides.

A practical approach to temperature effects in dissociative electron attachment cross sections using local complex potential theory

Energy Technology Data Exchange (ETDEWEB)

Sugioka, Yuji [Department of Chemistry, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570 (Japan); Takayanagi, Toshiyuki, E-mail: tako@mail.saitama-u.ac.jp [Department of Chemistry, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570 (Japan)

2012-09-11

Highlights: Black-Right-Pointing-Pointer Dissociative electron attachment cross sections for polyatomic molecules are calculated by a simple theoretical approach. Black-Right-Pointing-Pointer Temperature effects can be reasonably reproduced with the present model. Black-Right-Pointing-Pointer All the degrees-of-freedom are taken into account in the present dynamics approach. -- Abstract: We propose a practical computational scheme to obtain temperature dependence of dissociative electron attachment cross sections to polyatomic molecules within a local complex potential theory formalism. First we perform quantum path-integral molecular dynamics simulations on the potential energy surface for the neutral molecule in order to sample initial nuclear configurations as well as momenta. Classical trajectories are subsequently integrated on the potential energy surface for the anionic state and survival probabilities are simultaneously calculated along the obtained trajectories. We have applied this simple scheme to dissociative electron attachment processes to H{sub 2}O and CF{sub 3}Cl, for which several previous studies are available from both the experimental and theoretical sides.

Ultrafast dissociation: An unexpected tool for probing molecular dynamics

International Nuclear Information System (INIS)

Morin, Paul; Miron, Catalin

2012-01-01

Highlights: ► Ultrafast dissociation has been investigated by means of XPS and mass spectrometry. ► The interplay between electron relaxation and molecular dynamics is evidenced. ► Extension toward polyatomics, clusters, adsorbed molecules is considered. ► Quantum effects (spectral hole, angular effects) evidence the molecular field anisotropy. -- Abstract: Ultrafast dissociation following core–shell excitation into an antibonding orbital led to the early observation in HBr of atomic Auger lines associated to the decay of dissociated excited atoms. The purpose of this article is to review the very large variety of systems where such a situation has been encountered, extending from simple diatomic molecules toward more complex systems like polyatomics, clusters, or adsorbed molecules. Interestingly, this phenomenon has revealed an extremely rich and powerful tool for probing nuclear dynamics and its subtle interplay with electron relaxation occurring on a comparable time scale. Consequently this review covers a surprisingly large period, starting in 1986 and still ongoing.

Nano-manipulation of single DNA molecules

International Nuclear Information System (INIS)

Hu Jun; Shanghai Jiaotong Univ., Shanghai; Lv Junhong; Wang Guohua; Wang Ying; Li Minqian; Zhang Yi; Li Bin; Li Haikuo; An Hongjie

2004-01-01

Nano-manipulation of single atoms and molecules is a critical technique in nanoscience and nanotechnology. This review paper will focus on the recent development of the manipulation of single DNA molecules based on atomic force microscopy (AFM). Precise manipulation has been realized including varied manipulating modes such as 'cutting', 'pushing', 'folding', 'kneading', 'picking up', 'dipping', etc. The cutting accuracy is dominated by the size of the AFM tip, which is usually 10 nm or less. Single DNA fragments can be cut and picked up and then amplified by single molecule PCR. Thus positioning isolation and sequencing can be performed. (authors)

Entangled photons from single atoms and molecules

Science.gov (United States)

Nordén, Bengt

2018-05-01

The first two-photon entanglement experiment performed 50 years ago by Kocher and Commins (KC) provided isolated pairs of entangled photons from an atomic three-state fluorescence cascade. In view of questioning of Bell's theorem, data from these experiments are re-analyzed and shown sufficiently precise to confirm quantum mechanical and dismiss semi-classical theory without need for Bell's inequalities. Polarization photon correlation anisotropy (A) is useful: A is near unity as predicted quantum mechanically and well above the semi-classic range, 0 ⩽ A ⩽ 1 / 2 . Although yet to be found, one may envisage a three-state molecule emitting entangled photon pairs, in analogy with the KC atomic system. Antibunching in fluorescence from single molecules in matrix and entangled photons from quantum dots promise it be possible. Molecules can have advantages to parametric down-conversion as the latter photon distribution is Poissonian and unsuitable for producing isolated pairs of entangled photons. Analytical molecular applications of entangled light are also envisaged.

Computer simulation of molecular absorption spectra for asymmetric top molecules

International Nuclear Information System (INIS)

Bende, A.; Tosa, V.; Cosma, V.

2001-01-01

The effective Hamiltonian formalism has been used to develop a model for infrared multiple-photon absorption (IRMPA) process in asymmetric top molecules. Assuming a collisionless regime, the interaction between the molecule and laser field can be described by the time-dependent Schroedinger equation. By using the rotating wave approximation and Laplace transformation, the time-dependent problem reduces to a time-independent eigen problem for an effective Hamiltonian which can be solved only numerically for a real vibrational-rotational structure of polyatomic molecule. The vibrational-rotational structure is assumed to be an anharmonic oscillator coupled to an asymmetric rigid rotor. The main assumptions taken into account for this model are the following: (1) the excitation is coherent, i.e. the collision (if present during the laser pulse) does not influence the excitation; (2) the excitation starts from the ground state and is near resonant to a normal mode, thus, the rotating wave approximation can be applied; (3) after absorbing N photons the vibrational energy of the excited mode leak into a quasicontinuum; (4) the thermal population of the ground state is given by the Maxwell-Boltzmann distribution law. The energy levels of the asymmetric top molecules cannot be represented by an explicit formula analogous to that for the symmetric top, according to quantum mechanics, but we can consider it a deviation from the prolate or oblate case of the symmetric top, and we can find in the same manner the selection rules of the asymmetric case using the selection rules for the symmetric case. The infrared bands of asymmetric top molecules are not resolved, but if the dispersion used is not too small, so that the envelopes of the bands can be distinguished from simple maxima, it is possible to draw conclusions as to the type of the bands. In this case, the simulation of the absorption spectra can give us some important information about the types of these bands. In

Modulation of intermolecular interactions in single-molecule magnets

Science.gov (United States)

Heroux, Katie Jeanne

Polynuclear manganese clusters exhibiting interesting magnetic and quantum properties have been an area of intense research since the discovery of the first single-molecule magnet (SMM) in 1993. These molecules, below their blocking temperature, function as single-domain magnetic particles which exhibit classical macroscale magnetic properties as well as quantum mechanical phenomena such as quantum tunnelling of magnetization (QTM) and quantum phase interference. The union of classical and quantum behavior in these nanomaterials makes SMMs ideal candidates for high-density information storage and quantum computing. However, environmental coupling factors (nuclear spins, phonons, neighboring molecules) must be minimized if such applications are ever to be fully realized. The focus of this work is making small structural changes in well-known manganese SMMs in order to drastically enhance the overall magnetic and quantum properties of the system. Well-isolated molecules of high crystalline quality should lead to well-defined energetic and spectral properties as well. An advantage of SMMs over bulk magnetic materials is that they can be chemically altered from a "bottom-up" approach providing a synthetic tool for tuning magnetic properties. This systematic approach is utilized in the work presented herein by incorporating bulky ligands and/or counterions to "isolate" the magnetic core of [Mn4] dicubane SMMs. Reducing intermolecular interactions in the crystal lattice (neighboring molecules, solvate molecules, dipolar interactions) is an important step toward developing viable quantum computing devices. Detailed bulk magnetic studies as well as single crystal magnetization hysteresis and high-frequency EPR studies on these sterically-isolated complexes show enhanced, and sometimes even unexpected, quantum dynamics. The importance of intra- and intermolecular interactions remains a common theme throughout this work, extending to other SMMs of various topology including

Extended Thermodynamics of Rarefied Polyatomic Gases: 15-Field Theory Incorporating Relaxation Processes of Molecular Rotation and Vibration

Directory of Open Access Journals (Sweden)

Takashi Arima

2018-04-01

Full Text Available After summarizing the present status of Rational Extended Thermodynamics (RET of gases, which is an endeavor to generalize the Navier–Stokes and Fourier (NSF theory of viscous heat-conducting fluids, we develop the molecular RET theory of rarefied polyatomic gases with 15 independent fields. The theory is justified, at mesoscopic level, by a generalized Boltzmann equation in which the distribution function depends on two internal variables that take into account the energy exchange among the different molecular modes of a gas, that is, translational, rotational, and vibrational modes. By adopting the generalized Bhatnagar, Gross and Krook (BGK-type collision term, we derive explicitly the closed system of field equations with the use of the Maximum Entropy Principle (MEP. The NSF theory is derived from the RET theory as a limiting case of small relaxation times via the Maxwellian iteration. The relaxation times introduced in the theory are shown to be related to the shear and bulk viscosities and heat conductivity.

Enhanced sensitivity to a possible variation of the proton-to-electron mass ratio in ammonia

Czech Academy of Sciences Publication Activity Database

Owens, A.; Yurchenko, S. N.; Thiel, W.; Špirko, Vladimír

2016-01-01

Roč. 93, č. 5 (2016), č. článku 052506. ISSN 2469-9926 Institutional support: RVO:61388963 Keywords : precision measurements * polyatomic molecules * accurate prediction Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.925, year: 2016

Imaging and manipulation of a polar molecule on Ag(111)

DEFF Research Database (Denmark)

Lin, R.; Braun, K.F.; Tang, H.

2001-01-01

A scanning tunneling microscope (STM) was applied to image and laterally manipulate isolated phosphangulene molecules on Ag(111) at 6 K. Atomic-resolution images clearly revealed three characteristic types of appearances (three-lobed, fish and bump shape) for the adsorbed molecules, which could...

Single-base resolution and long-coverage sequencing based on single-molecule nanomanipulation

International Nuclear Information System (INIS)

An Hongjie; Huang Jiehuan; Lue Ming; Li Xueling; Lue Junhong; Li Haikuo; Zhang Yi; Li Minqian; Hu Jun

2007-01-01

We show new approaches towards a novel single-molecule sequencing strategy which consists of high-resolution positioning isolation of overlapping DNA fragments with atomic force microscopy (AFM), subsequent single-molecule PCR amplification and conventional Sanger sequencing. In this study, a DNA labelling technique was used to guarantee the accuracy in positioning the target DNA. Single-molecule multiplex PCR was carried out to test the contamination. The results showed that the two overlapping DNA fragments isolated by AFM could be successfully sequenced with high quality and perfect contiguity, indicating that single-base resolution and long-coverage sequencing have been achieved simultaneously

Impulsive Laser Induced Alignment of Molecules Dissolved in Helium Nanodroplets

DEFF Research Database (Denmark)

Pentlehner, Dominik; H. Nielsen, Jens; Slenczka, Alkwin

2013-01-01

We show that a 450 fs nonresonant, moderately intense, linearly polarized laser pulse can induce field-free molecular axis alignment of methyliodide (CH3I) molecules dissolved in a helium nanodroplet. Time-resolved measurements reveal rotational dynamics much slower than that of isolated molecules...

Small molecule fluoride toxicity agonists.

Science.gov (United States)

Nelson, James W; Plummer, Mark S; Blount, Kenneth F; Ames, Tyler D; Breaker, Ronald R

2015-04-23

Fluoride is a ubiquitous anion that inhibits a wide variety of metabolic processes. Here, we report the identification of a series of compounds that enhance fluoride toxicity in Escherichia coli and Streptococcus mutans. These molecules were isolated by using a high-throughput screen (HTS) for compounds that increase intracellular fluoride levels as determined via a fluoride riboswitch reporter fusion construct. A series of derivatives were synthesized to examine structure-activity relationships, leading to the identification of compounds with improved activity. Thus, we demonstrate that small molecule fluoride toxicity agonists can be identified by HTS from existing chemical libraries by exploiting a natural fluoride riboswitch. In addition, our findings suggest that some molecules might be further optimized to function as binary antibacterial agents when combined with fluoride. Copyright © 2015 Elsevier Ltd. All rights reserved.

Excited states 2

CERN Document Server

Lim, Edward C

2013-01-01

Excited States, Volume 2 is a collection of papers that deals with molecules in the excited states. The book describes the geometries of molecules in the excited electronic states. One paper describes the geometries of a diatomic molecule and of polyatomic molecules; it also discusses the determination of the many excited state geometries of molecules with two, three, or four atoms by techniques similar to diatomic spectroscopy. Another paper introduces an ordered theory related to excitons in pure and mixed molecular crystals. This paper also presents some experimental data such as those invo

High mass accuracy and high mass resolving power FT-ICR secondary ion mass spectrometry for biological tissue imaging

NARCIS (Netherlands)

Smith, D.F.; Kiss, A.; Leach, F.E.; Robinson, E.W.; Paša-Tolić, L.; Heeren, R.M.A.

2013-01-01

Biological tissue imaging by secondary ion mass spectrometry has seen rapid development with the commercial availability of polyatomic primary ion sources. Endogenous lipids and other small bio-molecules can now be routinely mapped on the sub-micrometer scale. Such experiments are typically

Calculations on the vibrational level density in highly excited formaldehyde

International Nuclear Information System (INIS)

Rashev, Svetoslav; Moule, David C.

2003-01-01

The object of the present work is to develop a model that provides realistic estimates of the vibrational level density in polyatomic molecules in a given electronic state, at very high (chemically relevant) vibrational excitation energies. For S 0 formaldehyde (D 2 CO), acetylene, and a number of triatomics, the estimates using conventional spectroscopic formulas have yielded densities at the dissociation threshold, very much lower than the experimentally measured values. In the present work we have derived a general formula for the vibrational energy levels of a polyatomic molecule, which is a generalization of the conventional Dunham spectroscopic expansion. Calculations were performed on the vibrational level density in S 0 D 2 CO, H 2 C 2 , and NO 2 at excitation energies in the vicinity of the dissociation limit, using the newly derived formula. The results from the calculations are in reasonable agreement with the experimentally measured data

A new crossed molecular beam apparatus using time-sliced ion velocity imaging technique

International Nuclear Information System (INIS)

Wu Guorong; Zhang Weiqing; Pan Huilin; Shuai Quan; Jiang Bo; Dai Dongxu; Yang Xueming

2008-01-01

A new crossed molecular beam apparatus has been constructed for investigating polyatomic chemical reactions using the time-sliced ion velocity map imaging technique. A unique design is adopted for one of the two beam sources and allows us to set up the molecular beam source either horizontally or vertically. This can be conveniently used to produce versatile atomic or radical beams from photodissociation and as well as electric discharge. Intensive H-atom beam source with high speed ratio was produced by photodissociation of the HI molecule and was reacted with the CD 4 molecule. Vibrational-state resolved HD product distribution was measured by detecting the CD 3 product. Preliminary results were also reported on the F+SiH 4 reaction using the discharged F atom beam. These results demonstrate that this new instrument is a powerful tool for investigating chemical dynamics of polyatomic reactions.

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

Science.gov (United States)

Stolow, Albert

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

Systematic studies of molecular vibrational anharmonicity and vibration-rotation interaction by self-consistent-field higher derivative methods: Applications to asymmetric and symmetric top and linear polyatomic molecules

International Nuclear Information System (INIS)

Clabo, D.A. Jr.

1987-04-01

Inclusion of the anharmonicity normal mode vibrations [i.e., the third and fourth (and higher) derivatives of a molecular Born-Oppenheimer potential energy surface] is necessary in order to theoretically reproduce experimental fundamental vibrational frequencies of a molecule. Although ab initio determinations of harmonic vibrational frequencies may give errors of only a few percent by the inclusion of electron correlation within a large basis set for small molecules, in general, molecular fundamental vibrational frequencies are more often available from high resolution vibration-rotation spectra. Recently developed analytic third derivatives methods for self-consistent-field (SCF) wavefunctions have made it possible to examine with previously unavailable accuracy and computational efficiency the anharmonic force fields of small molecules

Systematic studies of molecular vibrational anharmonicity and vibration-rotation interaction by self-consistent-field higher derivative methods: Applications to asymmetric and symmetric top and linear polyatomic molecules

Energy Technology Data Exchange (ETDEWEB)

Clabo, D.A. Jr.

1987-04-01

Inclusion of the anharmonicity normal mode vibrations (i.e., the third and fourth (and higher) derivatives of a molecular Born-Oppenheimer potential energy surface) is necessary in order to theoretically reproduce experimental fundamental vibrational frequencies of a molecule. Although ab initio determinations of harmonic vibrational frequencies may give errors of only a few percent by the inclusion of electron correlation within a large basis set for small molecules, in general, molecular fundamental vibrational frequencies are more often available from high resolution vibration-rotation spectra. Recently developed analytic third derivatives methods for self-consistent-field (SCF) wavefunctions have made it possible to examine with previously unavailable accuracy and computational efficiency the anharmonic force fields of small molecules.

On the Mass of Atoms in Molecules: Beyond the Born-Oppenheimer Approximation

Science.gov (United States)

Scherrer, Arne; Agostini, Federica; Sebastiani, Daniel; Gross, E. K. U.; Vuilleumier, Rodolphe

2017-07-01

Describing the dynamics of nuclei in molecules requires a potential energy surface, which is traditionally provided by the Born-Oppenheimer or adiabatic approximation. However, we also need to assign masses to the nuclei. There, the Born-Oppenheimer picture does not account for the inertia of the electrons, and only bare nuclear masses are considered. Nowadays, experimental accuracy challenges the theoretical predictions of rotational and vibrational spectra and requires the participation of electrons in the internal motion of the molecule. More than 80 years after the original work of Born and Oppenheimer, this issue has still not been solved, in general. Here, we present a theoretical and numerical framework to address this problem in a general and rigorous way. Starting from the exact factorization of the electron-nuclear wave function, we include electronic effects beyond the Born-Oppenheimer regime in a perturbative way via position-dependent corrections to the bare nuclear masses. This maintains an adiabaticlike point of view: The nuclear degrees of freedom feel the presence of the electrons via a single potential energy surface, whereas the inertia of electrons is accounted for and the total mass of the system is recovered. This constitutes a general framework for describing the mass acquired by slow degrees of freedom due to the inertia of light, bounded particles; thus, it is applicable not only in electron-nuclear systems but in light-heavy nuclei or ions as well. We illustrate this idea with a model of proton transfer, where the light particle is the proton and the heavy particles are the oxygen atoms to which the proton is bounded. Inclusion of the light-particle inertia allows us to gain orders of magnitude in accuracy. The electron-nuclear perspective is adopted, instead, to calculate position-dependent mass corrections using density functional theory for a few polyatomic molecules at their equilibrium geometry. These data can serve as input for the

On the Mass of Atoms in Molecules: Beyond the Born-Oppenheimer Approximation

Directory of Open Access Journals (Sweden)

Arne Scherrer

2017-08-01

Full Text Available Describing the dynamics of nuclei in molecules requires a potential energy surface, which is traditionally provided by the Born-Oppenheimer or adiabatic approximation. However, we also need to assign masses to the nuclei. There, the Born-Oppenheimer picture does not account for the inertia of the electrons, and only bare nuclear masses are considered. Nowadays, experimental accuracy challenges the theoretical predictions of rotational and vibrational spectra and requires the participation of electrons in the internal motion of the molecule. More than 80 years after the original work of Born and Oppenheimer, this issue has still not been solved, in general. Here, we present a theoretical and numerical framework to address this problem in a general and rigorous way. Starting from the exact factorization of the electron-nuclear wave function, we include electronic effects beyond the Born-Oppenheimer regime in a perturbative way via position-dependent corrections to the bare nuclear masses. This maintains an adiabaticlike point of view: The nuclear degrees of freedom feel the presence of the electrons via a single potential energy surface, whereas the inertia of electrons is accounted for and the total mass of the system is recovered. This constitutes a general framework for describing the mass acquired by slow degrees of freedom due to the inertia of light, bounded particles; thus, it is applicable not only in electron-nuclear systems but in light-heavy nuclei or ions as well. We illustrate this idea with a model of proton transfer, where the light particle is the proton and the heavy particles are the oxygen atoms to which the proton is bounded. Inclusion of the light-particle inertia allows us to gain orders of magnitude in accuracy. The electron-nuclear perspective is adopted, instead, to calculate position-dependent mass corrections using density functional theory for a few polyatomic molecules at their equilibrium geometry. These data can

Electron distributions of the first-row homonuclear diatomic molecules, A2

International Nuclear Information System (INIS)

Ramirez, B.I.; Bielefeld Univ.

1982-08-01

Electron momentum density contour maps of the first-row homonuclear diatomic molecules, A 2 , are obtained from near Hartree-Fock wave functions. Both the total momentum density and momentum density difference (molecule - isolated atoms) maps present trends that may be related to the binding in the molecules. These results are compared with the corresponding charge density maps in position space (Bader, Henneker and Cade 1967). (author)

Depolarization of fluorescence of polyatomic molecules in noble gas solvents

Science.gov (United States)

Blokhin, A. P.; Gelin, M. F.; Kalosha, I. I.; Matylitsky, V. V.; Erohin, N. P.; Barashkov, M. V.; Tolkachev, V. A.

2001-10-01

The collisional depolarization of fluorescence is studied for p-quarterphenyl (PQP) in He, Ar, Xe solvents, under pressures ranging from zero to nearly atmospheric. The results are interpreted within the Keilson-Storer model of the orientational relaxation and smooth rigid body collision dynamics. This allows us to estimate the rate of the angular momentum scrambling due to encounters of PQP with its partners. The collisions are shown to be neither strong nor weak, so that the averaged number of encounters giving rise to the PQP angular momentum randomization equals to 33 (PQP-He), 4.5 (PQP-Ar), and 2.1 (PQP-Xe).

Neutralizing antibody and anti-retroviral drug sensitivities of HIV-1 isolates resistant to small molecule CCR5 inhibitors

International Nuclear Information System (INIS)

Pugach, Pavel; Ketas, Thomas J.; Michael, Elizabeth; Moore, John P.

2008-01-01

The small molecule CCR5 inhibitors are a new class of drugs for treating infection by human immunodeficiency virus type 1 (HIV-1). They act by binding to the CCR5 co-receptor and preventing its use during HIV-1-cell fusion. Escape mutants can be raised against CCR5 inhibitors in vitro and will arise when these drugs are used clinically. Here, we have assessed the responses of CCR5 inhibitor-resistant viruses to other anti-retroviral drugs that act by different mechanisms, and their sensitivities to neutralizing antibodies (NAbs). The rationale for the latter study is that the resistance pathway for CCR5 inhibitors involves changes in the HIV-1 envelope glycoproteins (Env), which are also targets for NAbs. The escape mutants CC101.19 and D1/85.16 were selected for resistance to AD101 and vicriviroc (VVC), respectively, from the primary R5 HIV-1 isolate CC1/85. Each escape mutant was cross-resistant to other small molecule CCR5 inhibitors (aplaviroc, maraviroc, VVC, AD101 and CMPD 167), but sensitive to protein ligands of CCR5: the modified chemokine PSC-RANTES and the humanized MAb PRO-140. The resistant viruses also retained wild-type sensitivity to the nucleoside reverse transcriptase inhibitor (RTI) zidovudine, the non-nucleoside RTI nevirapine, the protease inhibitor atazanavir and other attachment and fusion inhibitors that act independently of CCR5 (BMS-806, PRO-542 and enfuvirtide). Of note is that the escape mutants were more sensitive than the parental CC1/85 isolate to a subset of neutralizing monoclonal antibodies and to some sera from HIV-1-infected people, implying that sequence changes in Env that confer resistance to CCR5 inhibitors can increase the accessibility of some NAb epitopes. The need to preserve NAb resistance may therefore be a constraint upon how escape from CCR5 inhibitors occurs in vivo

Molecular-beam studies of primary photochemical processes

Energy Technology Data Exchange (ETDEWEB)

Lee, Y.T.

1982-12-01

Application of the method of molecular-beam photofragmentation translational spectroscopy to the investigation of primary photochemical processes of polyatomic molecules is described. Examples will be given to illustrate how information concerning the energetics, dynamics, and mechanism of dissociation processes can be obtained from the precise measurements of angular and velocity distributions of products in an experiment in which a well-defined beam of molecules is crossed with a laser.

Molecular-beam studies of primary photochemical processes

International Nuclear Information System (INIS)

Lee, Y.T.

1982-12-01

Application of the method of molecular-beam photofragmentation translational spectroscopy to the investigation of primary photochemical processes of polyatomic molecules is described. Examples will be given to illustrate how information concerning the energetics, dynamics, and mechanism of dissociation processes can be obtained from the precise measurements of angular and velocity distributions of products in an experiment in which a well-defined beam of molecules is crossed with a laser

Study of open systems with molecules in isotropic liquids

Science.gov (United States)

Kondo, Yasushi; Matsuzaki, Masayuki

2018-05-01

We are interested in dynamics of a system in an environment, or an open system. Such phenomena as crossover from Markovian to non-Markovian relaxation and thermal equilibration are of our interest. Open systems have experimentally been studied with ultra cold atoms, ions in traps, optics, and cold electric circuits because well-isolated systems can be prepared here and thus the effects of environments can be controlled. We point out that some molecules solved in isotropic liquid are well isolated and thus they can also be employed for studying open systems in Nuclear Magnetic Resonance (NMR) experiments. First, we provide a short review on related phenomena of open systems that helps readers to understand our motivation. We, then, present two experiments as examples of our approach with molecules in isotropic liquids. Crossover from Markovian to non-Markovian relaxation was realized in one NMR experiment, while relaxation-like phenomena were observed in approximately isolated systems in the other.

Construction and maintenance of SUNY facilities at the National Synchrotron Light Source. Progress report, 1 July 1983-1 July 1984. Final report

International Nuclear Information System (INIS)

Bigeleisen, J.

1984-01-01

Research reported includes beamline facilities, X-21 beamline update, SUNY-PRT participation in the design and commissioning of the CHESS crystallography facility, surface physics, material and structure studies using EXAFS, x-ray standing wave studies of surfaces and interfaces, and surface diffraction of adsorbed polyatomic molecules

Application of the generator coordinates method to the intra-molecular proton tunneling in the malonaldehyde molecule; Aplicacao do metodo das coordenadas geradoras ao processo de tunelamento do proton intramolecular na molecula de malonaldeido

Energy Technology Data Exchange (ETDEWEB)

Schmidt, Andre Campos Kersten

1995-12-31

The effects of different vibrational modes on the isomerization process of polyatomic molecules, or solvent`s effects on reaction rates are object of up-to-date interest. In general, such many body phenomena are, in principle, multidimensional, and they first require a reduction of relevant degrees of freedom. In order to investigated, some aspects of the intra-molecular proton tunneling on a malonaldehyde molecule, we use the Generator Coordinate Method. The model used to describe such a process is the so-called System-Bath model, where the system is the reaction coordinate and the bath are the intrinsic degrees of freedom (vibrational modes of the molecule), which are described by a harmonic oscillator set linearly coupled to the system. The reduction of the multidimensional problem to the effective unidimensional one is done using a energy related variational principle on the intrinsic degrees of freedom. we obtained analytically a effective Hamiltonian where the effects of the various degrees of freedom reveal themselves in the appearance of a effective mass and in changes of the shape of the potential barrier. The analyticity of the method was crucial on identifying clearly the roles played by the different physical parameters involved. (author) 17 refs., 29 figs.

Isolation and Molecular Characterization of Biofouling Bacteria and Profiling of Quorum Sensing Signal Molecules from Membrane Bioreactor Activated Sludge

Directory of Open Access Journals (Sweden)

Harshad Lade

2014-02-01

Full Text Available The formation of biofilm in a membrane bioreactor depends on the production of various signaling molecules like N-acyl homoserine lactones (AHLs. In the present study, a total of 200 bacterial strains were isolated from membrane bioreactor activated sludge and screened for AHLs production using two biosensor systems, Chromobacterium violaceum CV026 and Agrobacterium tumefaciens A136. A correlation between AHLs production and biofilm formation has been made among screened AHLs producing strains. The 16S rRNA gene sequence analysis revealed the dominance of Aeromonas and Enterobacter sp. in AHLs production; however few a species of Serratia, Leclercia, Pseudomonas, Klebsiella, Raoultella and Citrobacter were also identified. The chromatographic characterization of sludge extract showed the presence of a broad range of quorum sensing signal molecules. Further identification of sludge AHLs by thin layer chromatography bioassay and high performance liquid chromatography confirms the presence of C4-HSL, C6-HSL, C8-HSL, 3-oxo-C8-HSL, C10-HSL, C12-HSL, 3-oxo-C12-HSL and C14-HSL. The occurrence of AHLs in sludge extract and dominance of Aeromonas and Enterobacter sp. in activated sludge suggests the key role of these bacterial strains in AHLs production and thereby membrane fouling.

Isolation and molecular characterization of biofouling bacteria and profiling of quorum sensing signal molecules from membrane bioreactor activated sludge.

Science.gov (United States)

Lade, Harshad; Paul, Diby; Kweon, Ji Hyang

2014-02-04

The formation of biofilm in a membrane bioreactor depends on the production of various signaling molecules like N-acyl homoserine lactones (AHLs). In the present study, a total of 200 bacterial strains were isolated from membrane bioreactor activated sludge and screened for AHLs production using two biosensor systems, Chromobacterium violaceum CV026 and Agrobacterium tumefaciens A136. A correlation between AHLs production and biofilm formation has been made among screened AHLs producing strains. The 16S rRNA gene sequence analysis revealed the dominance of Aeromonas and Enterobacter sp. in AHLs production; however few a species of Serratia, Leclercia, Pseudomonas, Klebsiella, Raoultella and Citrobacter were also identified. The chromatographic characterization of sludge extract showed the presence of a broad range of quorum sensing signal molecules. Further identification of sludge AHLs by thin layer chromatography bioassay and high performance liquid chromatography confirms the presence of C4-HSL, C6-HSL, C8-HSL, 3-oxo-C8-HSL, C10-HSL, C12-HSL, 3-oxo-C12-HSL and C14-HSL. The occurrence of AHLs in sludge extract and dominance of Aeromonas and Enterobacter sp. in activated sludge suggests the key role of these bacterial strains in AHLs production and thereby membrane fouling.

Effective charge model in the theory of infrared intensities and its application for study of charge di.stribution in the molecules of organometallic compounds

International Nuclear Information System (INIS)

Aleksanyan, V.T.; Samvelyan, S.Kh.

1984-01-01

General principles of plotting the parametric theory of IR spectrum intensities of polyatomic molecules are outlined. The development of the effective charges model in this theory is considered and the mathematical formalism of the first approximation of the method of effective atom charges is described in detail. The results of calculations of charges distribution in the Mo(CO) 6 , W(CO) 6 , Cp 2 V, Cp 2 Ru and others (Cp-cyclopentadiene), performed in the frame work of the outlined scheme are presented. It is shown that in the investigated carbonyles the effective charge on oxygen and metal atoms is negative, on carbon atom - positive. In dicyclopentavienyl complexes the effective charge on the metal atom is positive and is not over 0.6e; charge values on hydrogen and carbon atoms do not exceed, 0.10-0.15e. The notions of ''electrovalence'' of coordination bond and charge distribution in the case of metallocenes are not correlated

Interference in acetylene intersystem crossing acts as the molecular analog of Young's double-slit experiment

NARCIS (Netherlands)

de Groot, M.; Field, R.W.; Buma, W.J.

2009-01-01

We report on an experimental approach that reveals crucial details of the composition of singlet-triplet mixed eigenstates in acetylene. Intersystem crossing in this prototypical polyatomic molecule embodies the mixing of the lowest excited singlet state (S1) with 3 triplet states (T1, T2, and T3).

Semiclassical spectral quantization: Application to two and four coupled molecular degrees of freedom

International Nuclear Information System (INIS)

De Leon, N.; Heller, E.J.

1984-01-01

Semiclassical quantization of the quasiperiodic vibrational motion of molecules is usually based on Einstein--Brillouin--Keller (EBK) conditions for the quantization of the classical actions. Explicit use of the EBK conditions for molecular systems of K degrees of freedom requires K quantization conditions. Therefore, explicit use of the EBK conditions becomes increasingly difficult if not impossible for polyatomic systems of three or more degrees of freedom. In this paper we propose a semiclassical quantization method which makes explicit use of phase coherence of the de Broglie wave associated with the trajectory rather than the EBK conditions. We show that taking advantage of phase coherence reduces the K quantization conditions to a single quantum condition: regardless of the number of degrees of freedom. For reasons that will become obvious we call this method ''spectral quantization.'' Polyatomic vibrational wave functions and energy eigenvalues are generated from quasiperiodic classical trajectories. The spectral method is applied to an ABA linear triatomic molecule with two degrees of freedom and to an anharmonic model of the molecule cyanoacetylene. The usefulness of the technique is demonstrated in this latter calculation since the cyanoacetylene model will have four coupled vibrational degrees of freedom

Single-molecule conductance of redox molecules in electrochemical scanning tunneling microscopy

DEFF Research Database (Denmark)

Haiss, W.; Albrecht, Tim; van Zalinge, H.

2007-01-01

of a maximum in the I-tunneling versus electrode potential relationship can be fitted by a "soft" gating concept. This arises from large configurational fluctuations of the molecular bridge linked to the gold contacts by flexible chains. This view is incorporated in a formalism that is well-suited for data...... analysis and reproduces in all important respects the 6V6 data for physically sound values of the appropriate parameters. This study demonstrates that fluctuations of isolated configurationally "soft" molecules can dominate charge transport patterns and that theoretical frameworks for compact monolayers...

From isolated light-harvesting complexes to the thylakoid membrane: a single-molecule perspective

Science.gov (United States)

Gruber, J. Michael; Malý, Pavel; Krüger, Tjaart P. J.; Grondelle, Rienk van

2018-01-01

The conversion of solar radiation to chemical energy in plants and green algae takes place in the thylakoid membrane. This amphiphilic environment hosts a complex arrangement of light-harvesting pigment-protein complexes that absorb light and transfer the excitation energy to photochemically active reaction centers. This efficient light-harvesting capacity is moreover tightly regulated by a photoprotective mechanism called non-photochemical quenching to avoid the stress-induced destruction of the catalytic reaction center. In this review we provide an overview of single-molecule fluorescence measurements on plant light-harvesting complexes (LHCs) of varying sizes with the aim of bridging the gap between the smallest isolated complexes, which have been well-characterized, and the native photosystem. The smallest complexes contain only a small number (10-20) of interacting chlorophylls, while the native photosystem contains dozens of protein subunits and many hundreds of connected pigments. We discuss the functional significance of conformational dynamics, the lipid environment, and the structural arrangement of this fascinating nano-machinery. The described experimental results can be utilized to build mathematical-physical models in a bottom-up approach, which can then be tested on larger in vivo systems. The results also clearly showcase the general property of biological systems to utilize the same system properties for different purposes. In this case it is the regulated conformational flexibility that allows LHCs to switch between efficient light-harvesting and a photoprotective function.

Proteoglycan isolation and analysis

DEFF Research Database (Denmark)

Woods, A; Couchman, J R

2001-01-01

Proteoglycans can be difficult molecules to isolate and analyze due to large mass, charge, and tendency to aggregate or form macromolecular complexes. This unit describes detailed methods for purification of matrix, cell surface, and cytoskeleton-linked proteoglycans. Methods for analysis...

Pramana – Journal of Physics | Indian Academy of Sciences

Indian Academy of Sciences (India)

2014-02-12

Feb 12, 2014 ... We simulate adaptive feedback control to coherently shape a femtosecond infrared laser pulse by means of a 4f-spatial light modulator in order to selectively excite the rovibrational modes of a polyatomic molecule. We preferentially populate an arbitrarily chosen upper rovibrational level by only employing ...

Theoretical studies on nuclear spin selective quantum dynamics of non-linear molecules; Theoretische Untersuchung zur Quantendynamik der Kernspinisomere nicht-linearer Molekuele

Energy Technology Data Exchange (ETDEWEB)

Grohmann, Thomas

2012-05-31

In this thesis the wave packet dynamics of nuclear spin isomers of polyatomic molecules after interaction with static and time-dependent magnetic fields and moderate intense nonresonant laser pulses is investigated. In particular, the process of inducing (internal) molecular rotation as well as alignment of molecules by manipulating their rotational or rotational-torsional degrees of freedom is studied. In the first part of the thesis all theoretical concepts for identifying nuclear spin isomers and for describing their quantum dynamics will be discussed. Especially the symmetrization postulate and themolecular symmetry group will be introduced and illustrated for some examples of molecules. These concepts will be extended to the case of identifying nuclear spin isomers in the presence of an external field. In the second part it is shown for nitromethane that magnetic fields are able to induce unidirectional rotations in opposite directions for different nuclear spin isomers of molecules containing methyl groups if the dipolar interaction is included. Additionally, it is demonstrated that different nuclear spin isomers of a chemical compound may show different alignment after the interaction with a moderate intense laser pulse. As shown for the rigid symmetric top propadien and the rigid asymmetric tops ethene and analogues, distinct pairs of nuclear spin isomers show at certain points in time a complementary behavior: while one isomer is showing alignment the partner isomer is showing anti-alignment. Moreover, it is illustrated that not every nuclear spin isomer can be aligned equally efficient. The alignment of non-rigid molecules is considered as well. As an example for a molecule with feasible torsion in the electronic ground state, the alignment of diboron tetrafluoride is investigated. It becomes apparent that not only rotational but also the torsional dynamics of the molecules is nuclear spin selective; different nuclear spin isomers have at distinct points

Nonlinear Hamiltonian mechanics applied to molecular dynamics theory and computational methods for understanding molecular spectroscopy and chemical reactions

CERN Document Server

Farantos, Stavros C

2014-01-01

This brief presents numerical methods for describing and calculating invariant phase space structures, as well as solving the classical and quantum equations of motion for polyatomic molecules. Examples covered include simple model systems to realistic cases of molecules spectroscopically studied. Vibrationally excited and reacting molecules are nonlinear dynamical systems, and thus, nonlinear mechanics is the proper theory to elucidate molecular dynamics by investigating invariant structures in phase space. Intramolecular energy transfer, and the breaking and forming of a chemical bond have now found a rigorous explanation by studying phase space structures.

Recent progress in the theory of dissociative attachment: From diatomics to biomolecules

International Nuclear Information System (INIS)

Fabrikant, Ilya I

2010-01-01

We present a summary of recent progress in theoretical studies of low-energy dissociative electron attachment (DEA) to halogen molecules and polyatomic molecules based on the resonance R-matrix theory. It explains many observed features in DEA cross sections including low-energy behavior, threshold resonances and cusps. It also gives correct description of the temperature dependence of the attachment rate coefficients. More recently the theory was applied to two molecules of biological interest, formic acid and glycine. DEA mechanisms in these systems are very similar to those in hydrogen halides.

Live Cell Genomics: RNA Exon-Specific RNA-Binding Protein Isolation.

Science.gov (United States)

Bell, Thomas J; Eberwine, James

2015-01-01

RNA-binding proteins (RBPs) are essential regulatory proteins that control all modes of RNA processing and regulation. New experimental approaches to isolate these indispensable proteins under in vivo conditions are needed to advance the field of RBP biology. Historically, in vitro biochemical approaches to isolate RBP complexes have been useful and productive, but biological relevance of the identified RBP complexes can be imprecise or erroneous. Here we review an inventive experimental to isolate RBPs under the in vivo conditions. The method is called peptide nucleic acid (PNA)-assisted identification of RBP (PAIR) technology and it uses cell-penetrating peptides (CPPs) to deliver photo-activatible RBP-capture molecule to the cytoplasm of the live cells. The PAIR methodology provides two significant advantages over the most commonly used approaches: (1) it overcomes the in vitro limitation of standard biochemical approaches and (2) the PAIR RBP-capture molecule is highly selective and adaptable which allows investigators to isolate exon-specific RBP complexes. Most importantly, the in vivo capture conditions and selectivity of the RBP-capture molecule yield biologically accurate and relevant RBP data.

In vitro characterization of multivalent adhesion molecule 7-based inhibition of multidrug-resistant bacteria isolated from wounded military personnel

Science.gov (United States)

Krachler, Anne Marie; Mende, Katrin; Murray, Clinton; Orth, Kim

2012-01-01

Treatment of wounded military personnel at military medical centers is often complicated by colonization and infection of wounds with pathogenic bacteria. These include nosocomially transmitted, often multidrug-resistant pathogens such as Acinetobacter baumannii-calcoaceticus complex, Pseudomonas aeruginosa and extended spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae. We analyzed the efficacy of multivalent adhesion molecule (MAM) 7-based anti-adhesion treatment of host cells against aforementioned pathogens in a tissue culture infection model. Herein, we observed that a correlation between two important hallmarks of virulence, attachment and cytotoxicity, could serve as a useful predictor for the success of MAM7-based inhibition against bacterial infections. Initially, we characterized 20 patient isolates (five from each pathogen mentioned above) in terms of genotypic diversity, antimicrobial susceptibility and important hallmarks of pathogenicity (biofilm formation, attachment to and cytotoxicity toward cultured host cells). All isolates displayed a high degree of genotypic diversity, which was also reflected by large strain-to-strain variability in terms of biofilm formation, attachment and cytotoxicity within each group of pathogen. Using non-pathogenic bacteria expressing MAM7 or latex beads coated with recombinant MAM7 for anti-adhesion treatment, we showed a decrease in cytotoxicity, indicating that MAM7 has potential as a prophylactic agent to attenuate infection by multidrug-resistant bacterial pathogens. PMID:22722243

International conference on matrix isolation spectroscopy. Extended Abstracts

Energy Technology Data Exchange (ETDEWEB)

1977-07-01

Seventy-five extended abstracts are arranged under the following headings: generation of reactive species and their isolation in matrices, spectra of metal atoms and cluster formation, stable molecules in matrices, Raman- and IR-spectroscopy, high-temperature molecules, reactive matrices, relaxation phenomena studied in matrices, and physical properties of matrices. (DLC)

Attosecond electron dynamics in molecules and liquids

Science.gov (United States)

WöRner, Hans Jakob

The ultrafast motion of electrons and holes following light-matter interaction is fundamental to a broad range of chemical and biophysical processes. In this lecture, I will discuss some of our recent experiments that measure the atomic-scale motion of charge with attosecond temporal resolution (1 as = 10-18s). The first experiment is carried out on isolated, spatially oriented molecules in the gas phase. Using high-harmonic spectroscopy, we resolve the migration of an electron hole across the molecule with a resolution of 100 as and simultaneously demonstrate extensive control over charge migration. In the second class of experiments, we use an attosecond pulse train synchronized with a near-infrared laser pulse to temporally resolve the process of photoemission from molecules in the gas phase and from a liquid-water microjet, resolving electron transport through liquid water on the attosecond time scale.

Isolation of Biosurfactant Producing Bacteria from Oil Reservoirs

OpenAIRE

A Tabatabaee, M Mazaheri Assadi, AA Noohi,VA Sajadian

2005-01-01

Biosurfactants or surface-active compounds are produced by microoaganisms. These molecules reduce surface tension both aqueous solutions and hydrocarbon mixtures. In this study, isolation and identification of biosurfactant producing bacteria were assessed. The potential application of these bacteria in petroleum industry was investigated. Samples (crude oil) were collected from oil wells and 45 strains were isolated. To confirm the ability of isolates in biosurfactant production, haemolysis ...

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

Science.gov (United States)

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

2017-03-22

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

Quantum Behavior of Water Molecules Confined to Nanocavities in Gemstones.

Science.gov (United States)

Gorshunov, Boris P; Zhukova, Elena S; Torgashev, Victor I; Lebedev, Vladimir V; Shakurov, Gil'man S; Kremer, Reinhard K; Pestrjakov, Efim V; Thomas, Victor G; Fursenko, Dimitry A; Dressel, Martin

2013-06-20

When water is confined to nanocavities, its quantum mechanical behavior can be revealed by terahertz spectroscopy. We place H2O molecules in the nanopores of a beryl crystal lattice and observe a rich and highly anisotropic set of absorption lines in the terahertz spectral range. Two bands can be identified, which originate from translational and librational motions of the water molecule isolated within the cage; they correspond to the analogous broad bands in liquid water and ice. In the present case of well-defined and highly symmetric nanocavities, the observed fine structure can be explained by macroscopic tunneling of the H2O molecules within a six-fold potential caused by the interaction of the molecule with the cavity walls.

On a simple way to calculate electronic resonances for polyatomic molecules

Czech Academy of Sciences Publication Activity Database

Horáček, J.; Paidarová, Ivana; Čurík, Roman

2015-01-01

Roč. 143, č. 18 (2015), č. článku 184102. ISSN 0021-9606 R&D Projects: GA ČR GAP208/11/0452; GA MŠk LD14088 Institutional support: RVO:61388955 Keywords : analytical continuation * coupling-constant * diacetylene Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.894, year: 2015

Single photon excimer laser photodissociation of highly vibrationally excited polyatomic molecules

International Nuclear Information System (INIS)

Tiee, J.J.; Wampler, F.B.; Rice, W.W.

1980-01-01

The ir + uv photodissociation of SF 6 has been performed using CO 2 and ArF lasers. The two-color photolysis significantly enhances the photodissociation process over ArF irradiation alone and is found to preserve the initial isotopic specificity of the ir excitation process

Control strategies for laser separation of carbon isotopes

Indian Academy of Sciences (India)

Laser isotope separation (LIS) by infrared laser chemistry of polyatomic molecules has come a long way since its discovery. The last decade has seen considerable efforts in scaling up of the process for light elements like carbon, oxygen and silicon. These efforts aim at ways to improve both the enrichment factor and the ...

Implementation of polyatomic MCTDHF capability

Science.gov (United States)

Haxton, Daniel; Jones, Jeremiah; Rescigno, Thomas; McCurdy, C. William; Ibrahim, Khaled; Williams, Sam; Vecharynski, Eugene; Rouet, Francois-Henry; Li, Xiaoye; Yang, Chao

2015-05-01

The implementation of the Multiconfiguration Time-Dependent Hartree-Fock method for poly- atomic molecules using a cartesian product grid of sinc basis functions will be discussed. The focus will be on two key components of the method: first, the use of a resolution-of-the-identity approximation; sec- ond, the use of established techniques for triple Toeplitz matrix algebra using fast Fourier transform over distributed memory architectures (MPI 3D FFT). The scaling of two-electron matrix element transformations is converted from O(N4) to O(N log N) by including these components. Here N = n3, with n the number of points on a side. We test the prelim- inary implementation by calculating absorption spectra of small hydro- carbons, using approximately 16-512 points on a side. This work is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under the Early Career program, and by the offices of BES and Advanced Scientific Computing Research, under the SciDAC program.

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

Science.gov (United States)

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

2013-11-01

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

Observing single molecule chemical reactions on metal nanoparticles.

Energy Technology Data Exchange (ETDEWEB)

Emory, S. R. (Steven R.); Ambrose, W. Patrick; Goodwin, P. M. (Peter M); Keller, Richard A.

2001-01-01

We report the study of the photodecomposition of single Rhodamine 6G (R6G) dye molecules adsorbed on silver nanoparticles. The nanoparticles were immobilized and spatially isolated on polylysine-derivatized glass coverslips, and confocal laser microspectroscopy was used to obtain surface-enhanced Raman scattering (SERS) spectra from individual R6G molecules. The photodecomposition of these molecules was observed with 150-ms temporal resolution. The photoproduct was identified as graphitic carbon based on the appearance of broad SERS vibrational bands at 1592 cm{sup -1} and 1340 cm{sup -1} observed in both bulk and averaged single-molecule photoproduct spectra. In contrast, when observed at the single-molecule level, the photoproduct yielded sharp SERS spectra. The inhomogeneous broadening of the bulk SERS spectra is due to a variety of photoproducts in different surface orientations and is a characteristic of ensemble-averaged measurements of disordered systems. These single-molecule studies indicate a photodecomposition pathway by which the R6G molecule desorbs from the metal surface, an excited-state photoreaction occurs, and the R6G photoproduct(s) readsorbs to the surface. A SERS spectrum is obtained when either the intact R6G or the R6G photoproduct(s) are adsorbed on a SERS-active site. This work further illustrates the power of single-molecule spectroscopy (SMS) to reveal unique behaviors of single molecules that are not discernable with bulk measurements.

Photoelectron spectroscopy

International Nuclear Information System (INIS)

Price, W.C.

1974-01-01

A survey is given of the development of x-ray and ultraviolet photoelectron spectroscopy. Applications of photoelectron spectroscopy to studies of atomic electronic configurations are discussed, including photoelectron spectra of hydrides isoelectronic with the inert gases; photoelectron spectra of the halogen derivatives of methane; photoelectron spectra of multiple bonded diatomic molecules; spectra and structure of some multiple bonded polyatomic molecules; spectra and structure of triatomic molecules; and methods of orbital assignment of bands in photoelectron spectra. Physical aspects are considered, including intensities; selection rules; dependence of cross section on photoelectron energy; autoionization; angular distribution of photoelectrons; electron-molecule interactions; and transient species. (26 figures, 54 references) (U.S.)

Momentum densities in chemistry

International Nuclear Information System (INIS)

Coplan, M.A.; Tossell, J.A.; Moore, J.H.

1982-01-01

A principal interest of the Maryland (e,2e) group is the electronic structure of polyatomic molecules. Potentially, (e,2e) spectroscopy offers great advantages over conventional spectroscopy, photoelectron spectroscopy and even electron and x-ray diffraction. The realization of these advantages depends on the solution of a number of experimental and theoretical problems which are discussed here

Quenching reactions of electronically excited atoms

International Nuclear Information System (INIS)

Setser, D.W.

2001-01-01

The two-body, thermal quenching reactions of electronically excited atoms are reviewed using excited states of Ar, Kr, and Xe atoms as examples. State-specific interstate relaxation and excitation-transfer reactions with atomic colliders are discussed first. These results then are used to discuss quenching reactions of excited-state atoms with diatomic and polyatomic molecules, the latter have large cross sections, and the reactions can proceed by excitation transfer and by reactive quenching. Excited states of molecules are not considered; however, a table of quenching rate constants is given for six excited-state molecules in an appendix

Study by photo-ionization of some simple poly-atomic molecules and calculation of the Franck-Condon factors; Etude par photo-ionization de quelques molecules poly-atomiques simples et calcul des facteurs de Franck-Condon

Energy Technology Data Exchange (ETDEWEB)

Botter, R [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

1968-02-01

The photo-ionization yield curves for C{sub 2}H{sub 2}, C{sub 2}D{sub 2}, C{sub 2}H{sub 4} and C{sub 2}H{sub 2}D{sub 2} have been determined using a mass spectrometer coupled with an U.V. monochromator. Besides exhibiting a stair case structure near threshold due to the excitation of vibrational levels in the ion ground state, all the curves have broad maxima corresponding to auto-ionization phenomena. The ionization potentials of these molecules have been measured, together with the appearance potentials of the main ion-fragments. The excitation probabilities for the vibrational levels during ionization, or Franck-Condon factors, have been calculated for C{sub 2}H{sub 2} and C{sub 2}D{sub 2} using the method developed by Sharp and Rosenstock. Good agreement is generally obtained between the calculated values and those obtained experimentally from the photo-ionization yield curves. The preceding calculation method is then extended to the case where the electronic transition occurs with changes in the geometrical structure of the molecule (in particular, changes of symmetry). The Franck-Condon factors have been determined for NH{sub 3} (symmetry changes) and for H{sub 2}O (changes in the equilibrium angle). Calculations show that there is generally considerable excitation of the combination bands. (author) [French] Les courbes de rendement de photoionisation pour C{sub 2}H{sub 2}, C{sub 2}D{sub 2}, C{sub 2}H{sub 4} et C{sub 2}H{sub 2}D{sub 2} determinees a l'aide d'un spectrometre de masse auquel etait couple un monochromateur U.V. En plus d'une structure en escalier au voisinage du seuil, due a l'excitation de niveaux vibrationnels dans l'ion a l'etat fondamental, toutes les courbes presentent des maxima tres aplatis correspondant a des phenomenes d'auto-ionisation. Les potentiels d'ionisation de ces molecules ont ete mesures ainsi que les potentiels d'apparition des principaux ions fragments. Les probabilites d'excitation de niveaux de vibration au cours de l

Parasitic helminths: a pharmacopeia of anti-inflammatory molecules.

Science.gov (United States)

Johnston, M J G; MacDonald, J A; McKay, D M

2009-02-01

Infection with parasitic helminths takes a heavy toll on the health and well-being of humans and their domestic livestock, concomitantly resulting in major economic losses. Analyses have consistently revealed bioactive molecules in extracts of helminths or in their excretory/secretory products that modulate the immune response of the host. It is our view that parasitic helminths are an untapped source of immunomodulatory substances that, in pure form, could become new drugs (or models for drug design) to treat disease. Here, we illustrate the range of immunomodulatory molecules in selected parasitic trematodes, cestodes and nematodes, their impact on the immune cells in the host and how the host may recognize these molecules. There are many examples of the partial characterization of helminth-derived immunomodulatory molecules, but these have not yet translated into new drugs, reflecting the difficulty of isolating and fully characterizing proteins, glycoproteins and lipid-based molecules from small amounts of parasite material. However, this should not deter the investigator, since analytical techniques are now being used to accrue considerable structural information on parasite-derived molecules, even when only minute quantities of tissue are available. With the introduction of methodologies to purify and structurally-characterize molecules from small amounts of tissue and the application of high throughput immunological assays, one would predict that an assessment of parasitic helminths will yield a variety of novel drug candidates in the coming years.

Dielectric response of molecules in empirical tight-binding theory

Science.gov (United States)

Boykin, Timothy B.; Vogl, P.

2002-01-01

In this paper we generalize our previous approach to electromagnetic interactions within empirical tight-binding theory to encompass molecular solids and isolated molecules. In order to guarantee physically meaningful results, we rederive the expressions for relevant observables using commutation relations appropriate to the finite tight-binding Hilbert space. In carrying out this generalization, we examine in detail the consequences of various prescriptions for the position and momentum operators in tight binding. We show that attempting to fit parameters of the momentum matrix directly generally results in a momentum operator which is incompatible with the underlying tight-binding model, while adding extra position parameters results in numerous difficulties, including the loss of gauge invariance. We have applied our scheme, which we term the Peierls-coupling tight-binding method, to the optical dielectric function of the molecular solid PPP, showing that this approach successfully predicts its known optical properties even in the limit of isolated molecules.

Identification of a cytotoxic molecule in heat-modified citrus pectin.

Science.gov (United States)

Leclere, Lionel; Fransolet, Maude; Cambier, Pierre; El Bkassiny, Sandy; Tikad, Abdellatif; Dieu, Marc; Vincent, Stéphane P; Van Cutsem, Pierre; Michiels, Carine

2016-02-10

Modified forms of citrus pectin possess anticancer properties. However, their mechanism of action and the structural features involved remain unclear. Here, we showed that citrus pectin modified by heat treatment displayed cytotoxic effects in cancer cells. A fractionation approach was used aiming to identify active molecules. Dialysis and ethanol precipitation followed by HPLC analysis evidenced that most of the activity was related to molecules with molecular weight corresponding to low degree of polymerization oligogalacturonic acid. Heat-treatment of galacturonic acid also generated cytotoxic molecules. Furthermore, heat-modified galacturonic acid and heat-fragmented pectin contained the same molecule that induced cell death when isolated by HPLC separation. Mass spectrometry analyses revealed that 4,5-dihydroxy-2-cyclopenten-1-one was one cytotoxic molecule present in heat-treated pectin. Finally, we synthesized the enantiopure (4R,5R)-4,5-dihydroxy-2-cyclopenten-1-one and demonstrated that this molecule was cytotoxic and induced a similar pattern of apoptotic-like features than heat-modified pectin. Copyright © 2015 Elsevier Ltd. All rights reserved.

Laser isotope and isomer separations: History and trends

International Nuclear Information System (INIS)

Letok'ov, V.S.

1990-01-01

Paper will review history and principles of laser isotope and nuclear isomer separation: laser multistep photoionization of isotopic and isomeric atoms, laser IR-UV two-step photodissociation of molecules, laser IR multiphoton photodissociation of polyatomic molecules. The comparison and areas of applications of these methods will be considered. Paper will discuss a present state of art of technology of these methods in practical scale in various countries. In conclusion the trends of research in this field including applications of laser-separated isotopes and isomers will be considered

Generalization of the linear algebraic method to three dimensions

International Nuclear Information System (INIS)

Lynch, D.L.; Schneider, B.I.

1991-01-01

We present a numerical method for the solution of the Lippmann-Schwinger equation for electron-molecule collisions. By performing a three-dimensional numerical quadrature, this approach avoids both a basis-set representation of the wave function and a partial-wave expansion of the scattering potential. The resulting linear equations, analogous in form to the one-dimensional linear algebraic method, are solved with the direct iteration-variation method. Several numerical examples are presented. The prospect for using this numerical quadrature scheme for electron-polyatomic molecules is discussed

Interaction of slow electrons with high-pressure gases ('Quasi-liquids'): synthesis of our knowledge on slow electron-molecule interactions. Progress report

International Nuclear Information System (INIS)

McCorkle, D.L.; Christophorou, L.G.

1985-01-01

A crucial step in our efforts to develop not only a coherent picture of radiation interaction with matter, but also to understand radiation effects and mechanisms, as well as the effects of chemical pollutants and toxic compounds, is to relate the often abundant knowledge on isolated molecules (low pressure gases) to that on liquids or solids. To understand the roles of the physical and chemical properties of molecules in biological reactions, we must know how these isolated-molecule properties change as molecules are embedded in gradually thicker and thicker (denser and denser) gaseous and, finally, liquid environments. The work initiated by us both at the Physics Department of The University of Tennessee and at the Oak Ridge National Laboratory addresses itself to this question. At both places, high pressure (40 to approx.8000 kPa) electron swarm experiments are currently in operation yielding information as to the effects of the density and nature of the environment on fundamental electron-molecule interaction processes at densities intermediate to those corresponding to low pressure gases and liquids, and the gradual transition from isolated molecule to condensed phase behavior

Matrix isolation as a tool for studying interstellar chemical reactions

Science.gov (United States)

Ball, David W.; Ortman, Bryan J.; Hauge, Robert H.; Margrave, John L.

1989-01-01

Since the identification of the OH radical as an interstellar species, over 50 molecular species were identified as interstellar denizens. While identification of new species appears straightforward, an explanation for their mechanisms of formation is not. Most astronomers concede that large bodies like interstellar dust grains are necessary for adsorption of molecules and their energies of reactions, but many of the mechanistic steps are unknown and speculative. It is proposed that data from matrix isolation experiments involving the reactions of refractory materials (especially C, Si, and Fe atoms and clusters) with small molecules (mainly H2, H2O, CO, CO2) are particularly applicable to explaining mechanistic details of likely interstellar chemical reactions. In many cases, matrix isolation techniques are the sole method of studying such reactions; also in many cases, complexations and bond rearrangements yield molecules never before observed. The study of these reactions thus provides a logical basis for the mechanisms of interstellar reactions. A list of reactions is presented that would simulate interstellar chemical reactions. These reactions were studied using FTIR-matrix isolation techniques.

Heterogeneity of biofilms formed by nonmucoid Pseudomonas aeruginosa isolates from patients with cystic fibrosis

DEFF Research Database (Denmark)

Lee, Baoleri; Haagensen, Janus Anders Juul; Ciofu, O.

2005-01-01

lactone quorum-sensing molecules). Compared with wild-type strain PAO 1, most P. aeruginosa isolates demonstrated different degrees of reduction of adherence on polystyrene surfaces. The in vitro biofilm formation of isolates was investigated in a hydrodynamic flow system. Confocal laser scanning...... to phenotypic changes and in vitro biofilm formation. The physiological alterations were associated with a loss of motility (35% were nonmotile) and with decreased production of virulence factors (pyocyanin, proteases) and quorum-sensing molecules (45% of the isolates were unable to produce 3-O-C(12)-homoserine...

Observation of rotational revivals for iodine molecules in helium droplets using a near-adiabatic laser pulse

Science.gov (United States)

Shepperson, Benjamin; Chatterley, Adam S.; Christiansen, Lars; Søndergaard, Anders A.; Stapelfeldt, Henrik

2018-01-01

A 160-ps near-Gaussian, linearly polarized laser pulse is used to align iodine (I2) molecules embedded in helium nanodroplets. The rise time of the laser pulse is sufficiently long and smooth that the alignment, characterized by , behaves adiabatically during the pulse turnon. However, after the laser pulse has turned off stays above 0.50 and a recurrence structure occurs ˜650 ps later. Measurements on isolated (I2) molecules with identical laser pulses are used to identify, through analysis of the observed half- and full-rotational revivals, that the nonadiabatic postpulse alignment dynamics results from a mild truncation of the trailing edge of the laser pulse. This truncation establishes a well-defined starting time for coherent rotation, which leads to the revival structures observed both for isolated molecules and molecules in He droplets. In the latter case the time-dependent trace recorded here is compared to that obtained previously for a 450-fs alignment pulse. It is found that the observed revivals are very similar.

Zero-mode waveguide nanophotonic structures for single molecule characterization

Science.gov (United States)

Crouch, Garrison M.; Han, Donghoon; Bohn, Paul W.

2018-05-01

Single-molecule characterization has become a crucial research tool in the chemical and life sciences, but limitations, such as limited concentration range, inability to control molecular distributions in space, and intrinsic phenomena, such as photobleaching, present significant challenges. Recent developments in non-classical optics and nanophotonics offer promising routes to mitigating these restrictions, such that even low affinity (K D ~ mM) biomolecular interactions can be studied. Here we introduce and review specific nanophotonic devices used to support single molecule studies. Optical nanostructures, such as zero-mode waveguides (ZMWs), are usually fabricated in thin gold or aluminum films and serve to confine the observation volume of optical microspectroscopy to attoliter to zeptoliter volumes. These simple nanostructures allow individual molecules to be isolated for optical and electrochemical analysis, even when the molecules of interest are present at high concentration (µM–mM) in bulk solution. Arrays of ZMWs may be combined with optical probes such as single molecule fluorescence, single molecule fluorescence resonance energy transfer, and fluorescence correlation spectroscopy for distributed analysis of large numbers of single-molecule reactions or binding events in parallel. Furthermore, ZMWs may be used as multifunctional devices, for example by combining optical and electrochemical functions in a single discrete architecture to achieve electrochemical ZMWs. In this review, we will describe the optical properties, fabrication, and applications of ZMWs for single-molecule studies, as well as the integration of ZMWs into systems for chemical and biochemical analysis.

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

Energy Technology Data Exchange (ETDEWEB)

Soniat, Marielle; Rick, Steven W., E-mail: srick@uno.edu [Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148 (United States); Kumar, Revati [Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70808 (United States)

2015-07-28

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

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

International Nuclear Information System (INIS)

Soniat, Marielle; Rick, Steven W.; Kumar, Revati

2015-01-01

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

Electron collisions and rovibrational action spectroscopy of cold H3+ molecules

International Nuclear Information System (INIS)

Kreckel, H; Petrignani, A; Berg, M; Bing, D; Reinhardt, S; Altevogt, S; Buhr, H; Froese, M; Hoffmann, J; Jordon-Thaden, B; Krantz, C; Lestinsky, M; Mendes, M; Novotny, O; Novotny, S; Pedersen, H B; Orlov, D A; Mikosch, J; Wester, R; Plasil, R; GlosIk, J; Schwalm, D; Zajfman, D; Wolf, A

2007-01-01

Electron recombination of H 3 + has found a lot of attention due to its outstanding relevance for the chemistry of the interstellar medium (ISM) and its role as a benchmark for the treatment of dissociative recombination (DR) of polyatomic ions. We report DR measurements performed at the TSR storage ring utilizing a cryogenic ion trap injector. Furthermore, a chemical probing spectroscopy technique is described that allows for a very sensitive monitoring of the populated states inside the ion injector. Since H 3 + exists in two different nuclear spin modifications, a controlled manipulation of the ortho/para fraction is needed in order to perform state-selective measurements

Some kinetic and spectroscopic evidence on intramolecular relaxation processes in polyatomic molecules

International Nuclear Information System (INIS)

Quack, M.

1983-01-01

The description and definition of intramolecular vibrational relaxation processes is discussed within the framework of the quantum mechanical and statistical mechanical equations of motion. The evidence from quite different experimental sources is summarized under the common aspect of vibrational relaxation. Although much of the evidence remains ambiguous, there is good indication that a localized vibrational excitation relaxes typically in 0.1 to 10 picoseconds, which is long compared to many optical and reactive processes

Photo absorption studies of polyatomic molecules using Indus 1 synchrotron radiation source

International Nuclear Information System (INIS)

Saraswathy, P.; Sunanda, K.; Aparna, S.; Rajashekar, B.N.; Das, N.C.

2004-06-01

The Photophysics beamline is a medium resolution beamline designed for carrying out photo absorption and fluorescence experiments using the synchrotron radiation source Indus-l. This beamline has been commissioned recently and is in operation. An experimental setup for gas phase absorption studies has been developed and installed. Absorption spectra of a few polyatomicmolecules viz. benzene, ammonia, carbon disulphide and acetone were recorded in the wavelength region 1500 -3000 A. The results from this study indicated the satisfactory performance of the beam line as well as the experimental setup. Details of the first set of absorption experiments carried out are discussed in this report. (author)

Large Amplitude Motions in Polyatomic Molecule Spectra: Intramolecular Vibrational Redistribution and Isomerization

National Research Council Canada - National Science Library

Field, Robert

1997-01-01

Through Stimulated Emission Pumping (SEP) studies of highly excited vibrational levels of the electronic ground state of HCP, the spectroscopic signatures of bond breaking isomer/atom (HCP right arrow HPC...

Long-Lived Ultracold Molecules with Electric and Magnetic Dipole Moments

Science.gov (United States)

Rvachov, Timur M.; Son, Hyungmok; Sommer, Ariel T.; Ebadi, Sepehr; Park, Juliana J.; Zwierlein, Martin W.; Ketterle, Wolfgang; Jamison, Alan O.

2017-10-01

We create fermionic dipolar 23Na 6Li molecules in their triplet ground state from an ultracold mixture of 23Na and 6Li. Using magnetoassociation across a narrow Feshbach resonance followed by a two-photon stimulated Raman adiabatic passage to the triplet ground state, we produce 3 ×1 04 ground state molecules in a spin-polarized state. We observe a lifetime of 4.6 s in an isolated molecular sample, approaching the p -wave universal rate limit. Electron spin resonance spectroscopy of the triplet state was used to determine the hyperfine structure of this previously unobserved molecular state.

Metal atom oxidation laser

International Nuclear Information System (INIS)

Jensen, R.J.; Rice, W.W.; Beattie, W.H.

1975-01-01

A chemical laser which operates by formation of metal or carbon atoms and reaction of such atoms with a gaseous oxidizer in an optical resonant cavity is described. The lasing species are diatomic or polyatomic in nature and are readily produced by exchange or other abstraction reactions between the metal or carbon atoms and the oxidizer. The lasing molecules may be metal or carbon monohalides or monoxides

Vibrational motion in a symmetric, double minimum potential

DEFF Research Database (Denmark)

Spanget-Larsen, Jens

2015-01-01

Molecular vibrational motion in a symmetric, double minimum potential is treated by means of a quartic model potential, by reference to the tables published by Jaan Laane and the results of harmonic analyses for the stationary points. The inversion vibration of ammonia is treated in detail. - Not...... on the harmonic approximation for polyatomic molecules are appended. - Presented at a NORFA Workshop in Hirtshals, Denmark, August 1997....

Femtosecond photodissociation dynamics of I studied by ion imaging

DEFF Research Database (Denmark)

Larsen, J.J.; Bjerre, N.; Mørkbak, N.J.

1998-01-01

on imaging is employed to analyze the fragments from timed Coulomb explosion studies of femtosecond (fs) molecular dynamics. The technique provides high detection efficiency and direct recording of the two-dimensional velocity of all ionized fragments. We illustrate the approach by studying...... agreement with quantum mechanical wave packet simulations. We discuss the perspectives for extending the studies to photochemical reactions of small polyatomic molecules...

Isolation of reovirus T3D mutants capable of infecting human tumor cells independent of junction adhesion molecule-A.

Directory of Open Access Journals (Sweden)

Diana J M van den Wollenberg

Full Text Available Mammalian Reovirus is a double-stranded RNA virus with a distinctive preference to replicate in and lyse transformed cells. On that account, Reovirus type 3 Dearing (T3D is clinically evaluated as oncolytic agent. The therapeutic efficacy of this approach depends in part on the accessibility of the reovirus receptor Junction Adhesion Molecule-A (JAM-A on the target cells. Here, we describe the isolation and characterization of reovirus T3D mutants that can infect human tumor cells independent of JAM-A. The JAM-A-independent (jin mutants were isolated on human U118MG glioblastoma cells, which do not express JAM-A. All jin mutants harbour mutations in the S1 segments close to the region that encodes the sialic acid-binding pocket in the shaft of the spike protein. In addition, two of the jin mutants encode spike proteins with a Q336R substitution in their head domain. The jin mutants can productively infect a wide range of cell lines that resist wt reovirus T3D infection, including chicken LMH cells, hamster CHO cells, murine endothelioma cells, human U2OS and STA-ET2.1 cells, but not primary human fibroblasts. The jin-mutants rely on the presence of sialic-acid residues on the cell surface for productive infection, as is evident from wheat germ agglutinin (WGA inhibition experiments, and from the jin-reovirus resistance of CHO-Lec2 cells, which have a deficiency of sialic-acids on their glycoproteins. The jin mutants may be useful as oncolytic agents for use in tumors in which JAM-A is absent or inaccessible.

Building one molecule from a reservoir of two atoms.

Science.gov (United States)

Liu, L R; Hood, J D; Yu, Y; Zhang, J T; Hutzler, N R; Rosenband, T; Ni, K-K

2018-05-25

Chemical reactions typically proceed via stochastic encounters between reactants. Going beyond this paradigm, we combined exactly two atoms in a single, controlled reaction. The experimental apparatus traps two individual laser-cooled atoms [one sodium (Na) and one cesium (Cs)] in separate optical tweezers and then merges them into one optical dipole trap. Subsequently, photoassociation forms an excited-state NaCs molecule. The discovery of previously unseen resonances near the molecular dissociation threshold and measurement of collision rates are enabled by the tightly trapped ultracold sample of atoms. As laser-cooling and trapping capabilities are extended to more elements, the technique will enable the study of more diverse, and eventually more complex, molecules in an isolated environment, as well as synthesis of designer molecules for qubits. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Molecule Matters van der Waals Molecules

Indian Academy of Sciences (India)

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

Investigation into the behavior of metal-argon polyatomic ions (MAr+) in the extraction region of inductively coupled plasma-mass spectrometry

International Nuclear Information System (INIS)

Ebert, Chris H.; Witte, Travis M.; Houk, R.S.

2012-01-01

The abundances of metal-argon polyatomic ions (MAr + ) are determined in inductively coupled plasma-mass spectrometry (ICP-MS). The ratios of MAr + abundance to that for M + ions are measured experimentally. These ratios are compared to expected values, calculated for typical plasma conditions using spectroscopic data. For all metals studied (Ti, V, Cr, Mn, Fe, Co, Ni, Cu, and Zn), the measured ratios are significantly lower than the calculated ratios. Increasing the plasma potential (and thereby increasing the ion kinetic energy) by means of a homemade guard electrode with a wide gap further reduces the MAr + /M + ratio. Implementing a skimmer cone designed for high transmission of light ions increases the MAr + abundance. Considering this evidence, the scarcity of MAr + ions is attributed to collision induced dissociation (CID), likely due to a shock wave at the tip of or in the throat of the skimmer cone. - Highlights: ► MAr + ions are less abundant in the mass spectrum than expected from the ICP. ► Increasing the plasma potential reduces their abundance further. ► The extraction lens voltage does not greatly affect the MAr + abundances. ► The weakly-bound MAr + ions are probably dissociated by collisions during extraction.

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

Energy Technology Data Exchange (ETDEWEB)

Ngo, Anh T.; Skeini, Timur [Nanoscale; amp, Quantum Phenomena Institute and Physics & amp, Astronomy Department, Ohio University, Athens, Ohio 45701, United States; Iancu, Violeta [Nanoscale; amp, Quantum Phenomena Institute and Physics & amp, Astronomy Department, Ohio University, Athens, Ohio 45701, United States; Redfern, Paul C.; Curtiss, Larry A.; Hla, Saw Wai [Nanoscale; amp, Quantum Phenomena Institute and Physics & amp, Astronomy Department, Ohio University, Athens, Ohio 45701, United States

2018-01-11

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

Identification and characterization of small molecule modulators of the Epstein-Barr virus-induced gene 2 (EBI2) receptor

DEFF Research Database (Denmark)

Gessier, Francois; Preuss, Inga; Yin, Hong

2014-01-01

immune response and has been genetically linked to autoimmune diseases such as type I diabetes ( Nature 2010 , 467 , 460 ). Here we describe the isolation of a potent small molecule antagonist for the EBI2 receptor. First, we identified a small molecule agonist NIBR51 (1), which enabled identification...

Evaporation of Lennard-Jones fluids.

Science.gov (United States)

Cheng, Shengfeng; Lechman, Jeremy B; Plimpton, Steven J; Grest, Gary S

2011-06-14

Evaporation and condensation at a liquid/vapor interface are ubiquitous interphase mass and energy transfer phenomena that are still not well understood. We have carried out large scale molecular dynamics simulations of Lennard-Jones (LJ) fluids composed of monomers, dimers, or trimers to investigate these processes with molecular detail. For LJ monomers in contact with a vacuum, the evaporation rate is found to be very high with significant evaporative cooling and an accompanying density gradient in the liquid domain near the liquid/vapor interface. Increasing the chain length to just dimers significantly reduces the evaporation rate. We confirm that mechanical equilibrium plays a key role in determining the evaporation rate and the density and temperature profiles across the liquid/vapor interface. The velocity distributions of evaporated molecules and the evaporation and condensation coefficients are measured and compared to the predictions of an existing model based on kinetic theory of gases. Our results indicate that for both monatomic and polyatomic molecules, the evaporation and condensation coefficients are equal when systems are not far from equilibrium and smaller than one, and decrease with increasing temperature. For the same reduced temperature T/T(c), where T(c) is the critical temperature, these two coefficients are higher for LJ dimers and trimers than for monomers, in contrast to the traditional viewpoint that they are close to unity for monatomic molecules and decrease for polyatomic molecules. Furthermore, data for the two coefficients collapse onto a master curve when plotted against a translational length ratio between the liquid and vapor phase.

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

Energy Technology Data Exchange (ETDEWEB)

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

2009-05-07

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

Molecule Matters van der Waals Molecules

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 15; Issue 7. Molecule Matters van der Waals Molecules - Rg•••HF Complexes are Debye Molecules! E Arunan. Feature Article Volume 15 Issue 7 July 2010 pp 667-674. Fulltext. Click here to view fulltext PDF. Permanent link:

Attosecond dynamics of electrons in molecules and liquids

Science.gov (United States)

Woerner, Hans Jakob

2016-05-01

The ultrafast motion of electrons and holes following light-matter interaction is fundamental to a broad range of chemical and biophysical processes. In this lecture, I will discuss two recent experiments carried out in our group that measure the atomic-scale motion of charge with attosecond temporal resolution (1 as = 10-18 s). The first experiment is carried out on isolated, spatially oriented molecules in the gas phase. We advance high-harmonic spectroscopy to resolve spatially and temporally the migration of an electron hole immediately following ionization of iodoacetylene, while simultaneously demonstrating extensive control over the process. A multidimensional approach, based on the measurement of both even and odd harmonic orders, enables us to reconstruct both quantum amplitudes and phases of the electronic states with a resolution of ~ 100 as. We separately reconstruct quasi-field-free and laser-controlled charge migration as a function of the spatial orientation of the molecule and determine the shape of the hole created by ionization. The second experiment is carried out on a free-flowing microjet of liquid water. We use an attosecond pulse train synchronized with a near-infrared laser pulse to temporally resolve the process of photoemission from liquid water using the RABBIT technique. We measure a delay on the order of 50 as between electrons emitted from the HOMO of liquid water compared to that of gas-phase water and a substantially reduced modulation contrast of the corresponding sidebands. Since our measurements on solvated water molecules are referenced to isolated ones, the measured delays reflect (i) the photoionization delays caused by electron transport through the aqueous environment and (ii) the effect of solvation on the parent molecule. The relative modulation contrast, in turn, contains information on (iii) the modification of transition amplitudes and (iv) dephasing processes. These experiments make the liquid phase and its fascinating

''Crown molecules'' for separating cesium

International Nuclear Information System (INIS)

Dozol, J.F.; Lamare, V.

2002-01-01

After the minor actinides, the second category of radionuclides that must be isolated to optimize nuclear waste management concerns fission products, especially two cesium isotopes. If the cesium-135 isotope could be extracted, it could subsequently be transmuted or conditioned using a tailor-made process. Eliminating the 137 isotope from reprocessing and nuclear facility-dismantling waste would allow to dispose of most of this waste in near-surface facilities, and simply process the small remaining quantity containing long-lived elements. CEA research teams and their international partners have thought up crown molecules that could be used to pick out the cesium and meet these objectives. (authors)

Ultrafast molecular imaging by laser-induced electron diffraction

International Nuclear Information System (INIS)

Peters, M.; Nguyen-Dang, T. T.; Cornaggia, C.; Saugout, S.; Charron, E.; Keller, A.; Atabek, O.

2011-01-01

We address the feasibility of imaging geometric and orbital structures of a polyatomic molecule on an attosecond time scale using the laser-induced electron diffraction (LIED) technique. We present numerical results for the highest molecular orbitals of the CO 2 molecule excited by a near-infrared few-cycle laser pulse. The molecular geometry (bond lengths) is determined within 3% of accuracy from a diffraction pattern which also reflects the nodal properties of the initial molecular orbital. Robustness of the structure determination is discussed with respect to vibrational and rotational motions with a complete interpretation of the laser-induced mechanisms.

Which radionuclide, carrier molecule and clinical indication for alpha-immunotherapy?

International Nuclear Information System (INIS)

Guerard, F.; Barbet, J.; Cherel, M.; Chatal, J.-F.; Haddad, F.; Kraeber-Bodere, F.

2015-01-01

Beta-emitting radionuclides are not able to kill isolated tumor cells disseminated in the body, even if a high density of radiolabeled molecules can be targeted at the surface of these cells because the vast majority of emitted electrons deliver their energy outside the targeted cells. Alpha-particle emitting radionuclides may overcome this limitation. It is thus of primary importance to test and validate the radionuclide of choice, the most appropriate carrier molecule and the most promising clinical indication. Four α-particle emitting radionuclides have been or are clinically tested in phase I studies namely 213 Bi, 225 Ac, 212 Pb and 211 At. Clinical safety has been documented and encouraging efficacy has been shown for some of them ( 213 Bi and 211 At). 211 At has been the most studied and could be the most promising radionuclide but 225 Ac and 212 Pb are also of potential great interest. Any carrier molecule that has been labeled with β-emitting radionuclides could be labeled with alpha particle-emitting radionuclide using, for some of them, the same chelating agents. However, the physical half-life of the radionuclide should match the biological half-life of the radioconjugate or its catabolites. Finally everybody agrees, based on the quite short range of alpha particles, on the fact that the clinical indications for alpha-immunotherapy should be limited to the situation of disseminated minimal residual diseases made of small clusters of malignant cells or isolated tumor cells.

A variable hard sphere-based phenomenological inelastic collision model for rarefied gas flow simulations by the direct simulation Monte Carlo method

Energy Technology Data Exchange (ETDEWEB)

Prasanth, P S; Kakkassery, Jose K; Vijayakumar, R, E-mail: y3df07@nitc.ac.in, E-mail: josekkakkassery@nitc.ac.in, E-mail: vijay@nitc.ac.in [Department of Mechanical Engineering, National Institute of Technology Calicut, Kozhikode - 673 601, Kerala (India)

2012-04-01

A modified phenomenological model is constructed for the simulation of rarefied flows of polyatomic non-polar gas molecules by the direct simulation Monte Carlo (DSMC) method. This variable hard sphere-based model employs a constant rotational collision number, but all its collisions are inelastic in nature and at the same time the correct macroscopic relaxation rate is maintained. In equilibrium conditions, there is equi-partition of energy between the rotational and translational modes and it satisfies the principle of reciprocity or detailed balancing. The present model is applicable for moderate temperatures at which the molecules are in their vibrational ground state. For verification, the model is applied to the DSMC simulations of the translational and rotational energy distributions in nitrogen gas at equilibrium and the results are compared with their corresponding Maxwellian distributions. Next, the Couette flow, the temperature jump and the Rayleigh flow are simulated; the viscosity and thermal conductivity coefficients of nitrogen are numerically estimated and compared with experimentally measured values. The model is further applied to the simulation of the rotational relaxation of nitrogen through low- and high-Mach-number normal shock waves in a novel way. In all cases, the results are found to be in good agreement with theoretically expected and experimentally observed values. It is concluded that the inelastic collision of polyatomic molecules can be predicted well by employing the constructed variable hard sphere (VHS)-based collision model.

Magnetic field modification of ultracold molecule-molecule collisions

International Nuclear Information System (INIS)

Tscherbul, T V; Suleimanov, Yu V; Aquilanti, V; Krems, R V

2009-01-01

We present an accurate quantum mechanical study of molecule-molecule collisions in the presence of a magnetic field. The work focuses on the analysis of elastic scattering and spin relaxation in collisions of O 2 ( 3 Σ g - ) molecules at cold (∼0.1 K) and ultracold (∼10 -6 K) temperatures. Our calculations show that magnetic spin relaxation in molecule-molecule collisions is extremely efficient except at magnetic fields below 1 mT. The rate constant for spin relaxation at T=0.1 K and a magnetic field of 0.1 T is found to be as large as 6.1x10 -11 cm -3 s -1 . The magnetic field dependence of elastic and inelastic scattering cross sections at ultracold temperatures is dominated by a manifold of Feshbach resonances with the density of ∼100 resonances per Tesla for collisions of molecules in the absolute ground state. This suggests that the scattering length of ultracold molecules in the absolute ground state can be effectively tuned in a very wide range of magnetic fields. Our calculations demonstrate that the number and properties of the magnetic Feshbach resonances are dramatically different for molecules in the absolute ground and excited spin states. The density of Feshbach resonances for molecule-molecule scattering in the low-field-seeking Zeeman state is reduced by a factor of 10.

Synthesis of Zn-MOF incorporating titanium-hydrides as active sites binding H{sub 2} molecules

Energy Technology Data Exchange (ETDEWEB)

Kim, Jongsik, E-mail: jkim40@nd.edu [Department of Chemical and Biomolecular Engineering, University of Notre Dame, 182, Fitzpatrick Hall, Notre Dame, IN 46556 (United States); Ok Kim, Dong; Wook Kim, Dong; Sagong, Kil [Hanwha Chemical Research & Development Center, 6, Shinseong-dong, Yuseong-gu, Daejeon 305-804 (Korea, Republic of)

2015-10-15

This paper describes the synthetic effort for a Zn-MOF imparting Ti-H as a preferential binding site potentially capturing H{sub 2} molecules via Kubas-type interaction. The formation mechanism of Ti-H innate to the final material was potentially demonstrated to follow a radical dissociation rather than a β-hydrogen elimination and a C-H reductive elimination. - Graphical abstract: This study details the synthesis and the formation mechanism of Zn-MOF adsorbent site-isolating TiH{sub 3} that can potentially capture H{sub 2} molecules via Kubas-binding mechanism. - Highlights: • OH-functionalized Zn-MOF was employed as a reactive template to site-isolate TiH{sub 3}. • This MOF was post-synthetically modified using a tetracyclohexyl titanium (IV). • This intermediate was hydrogenolyzed to change ligand from cyclohexyl to hydride. • Formation mechanism of TiH{sub 3} was investigated via two control GC–MS experiments. • Final Zn-MOF potentially site-isolating TiH{sub 3} species was used as a H{sub 2} adsorbent.

Study of the Mechanical Properties and Vibration Isolation Performance of a Molecular Spring Isolator

Directory of Open Access Journals (Sweden)

Muchun Yu

2016-01-01

Full Text Available Molecular Spring Isolator (MSI is a novel passive vibration isolation technique, providing High-Static-Low-Dynamic (HSLD stiffness based on the use of molecular spring material. The molecular spring material is a solid-liquid mixture consisting of water and hydrophobic nanoporous materials. Under a certain level of external pressure, water molecules can intrude into the hydrophobic pores of nanoporous materials, developing an additional solid-liquid interface. Such interfaces are able to store, release, and transform mechanical energy, providing properties like mechanical spring. Having been only recently developed, the basic mechanic properties of a MSI have not been studied in depth. This paper focuses on the stiffness influence factors, the dynamic frequency response, and the vibration isolation performance of a MSI; these properties help engineers to design MSIs for different engineering applications. First, the working mechanism of a MSI is introduced from a three-dimensional general view of the water infiltration massive hydrophobic nanoporous pores. Next, a wide range of influence factors on the stiffness properties of MSI are studied. In addition, the frequency response functions (FRFs of the MSI vibration isolation system are studied utilizing the matching method based on equivalent piecewise linear (EPL system. Finally, the vibration isolation properties of MSI are evaluated by force transmissibility.

Detecting high-density ultracold molecules using atom–molecule collision

International Nuclear Information System (INIS)

Chen, Jun-Ren; Kao, Cheng-Yang; Chen, Hung-Bin; Liu, Yi-Wei

2013-01-01

Utilizing single-photon photoassociation, we have achieved ultracold rubidium molecules with a high number density that provides a new efficient approach toward molecular quantum degeneracy. A new detection mechanism for ultracold molecules utilizing inelastic atom–molecule collision is demonstrated. The resonant coupling effect on the formation of the X 1 Σ + g ground state 85 Rb 2 allows for a sufficient number of more deeply bound ultracold molecules, which induced an additional trap loss and heating of the co-existing atoms owing to the inelastic atom–molecule collision. Therefore, after the photoassociation process, the ultracold molecules can be investigated using the absorption image of the ultracold rubidium atoms mixed with the molecules in a crossed optical dipole trap. The existence of the ultracold molecules was then verified, and the amount of accumulated molecules was measured. This method detects the final produced ultracold molecules, and hence is distinct from the conventional trap loss experiment, which is used to study the association resonance. It is composed of measurements of the time evolution of an atomic cloud and a decay model, by which the number density of the ultracold 85 Rb 2 molecules in the optical trap was estimated to be >5.2 × 10 11 cm −3 . (paper)

Effects of 31 FDA approved small-molecule kinase inhibitors on isolated rat liver mitochondria.

Science.gov (United States)

Zhang, Jun; Salminen, Alec; Yang, Xi; Luo, Yong; Wu, Qiangen; White, Matthew; Greenhaw, James; Ren, Lijun; Bryant, Matthew; Salminen, William; Papoian, Thomas; Mattes, William; Shi, Qiang

2017-08-01

The FDA has approved 31 small-molecule kinase inhibitors (KIs) for human use as of November 2016, with six having black box warnings for hepatotoxicity (BBW-H) in product labeling. The precise mechanisms and risk factors for KI-induced hepatotoxicity are poorly understood. Here, the 31 KIs were tested in isolated rat liver mitochondria, an in vitro system recently proposed to be a useful tool to predict drug-induced hepatotoxicity in humans. The KIs were incubated with mitochondria or submitochondrial particles at concentrations ranging from therapeutic maximal blood concentrations (Cmax) levels to 100-fold Cmax levels. Ten endpoints were measured, including oxygen consumption rate, inner membrane potential, cytochrome c release, swelling, reactive oxygen species, and individual respiratory chain complex (I-V) activities. Of the 31 KIs examined only three including sorafenib, regorafenib and pazopanib, all of which are hepatotoxic, caused significant mitochondrial toxicity at concentrations equal to the Cmax, indicating that mitochondrial toxicity likely contributes to the pathogenesis of hepatotoxicity associated with these KIs. At concentrations equal to 100-fold Cmax, 18 KIs were found to be toxic to mitochondria, and among six KIs with BBW-H, mitochondrial injury was induced by regorafenib, lapatinib, idelalisib, and pazopanib, but not ponatinib, or sunitinib. Mitochondrial liability at 100-fold Cmax had a positive predictive power (PPV) of 72% and negative predictive power (NPV) of 33% in predicting human KI hepatotoxicity as defined by product labeling, with the sensitivity and specificity being 62% and 44%, respectively. Similar predictive power was obtained using the criterion of Cmax ≥1.1 µM or daily dose ≥100 mg. Mitochondrial liability at 1-2.5-fold Cmax showed a 100% PPV and specificity, though the NPV and sensitivity were 32% and 14%, respectively. These data provide novel mechanistic insights into KI hepatotoxicity and indicate that

Discovery of the First Interstellar Chiral Molecule: Propylene Oxide

Science.gov (United States)

Carroll, Brandon; McGuire, Brett A.; Loomis, Ryan; Finneran, Ian A.; Jewell, Philip; Remijan, Anthony; Blake, Geoffrey

2016-06-01

Life on Earth relies on chiral molecules, that is, species not superimposable on their mirror images. This manifests itself as a reliance on a single molecular handedness, or homochirality that is characteristic of life and perhaps most readily apparent in the large enhancement in biological activity of particular amino acid and sugar enantiomers. Yet, the ancestral origin of biological homochirality remains a mystery. The non-racemic ratios in some organics isolated from primitive meteorites hint at a primordial chiral seed but even these samples have experienced substantial processing during planetary assembly, obscuring their complete histories. To determine the underlying origin of any enantiomeric excess, it is critical to understand the molecular gas from which these molecules originated. Here, we present the first extra-solar, astronomical detection of a chiral molecule, propylene oxide (CH_3CHCH_2O), in absorption toward the Galactic Center. With the detection of propylene oxide, we at last have a target for broad-ranging searches for the possible cosmic origin of the homochirality of life.

A systematization of spectral data on the methanol molecule

Science.gov (United States)

Akhlyostin, A. Yu.; Voronina, S. S.; Lavrentiev, N. A.; Privezentsev, A. I.; Rodimova, O. B.; Fazliev, A. Z.

2015-11-01

Problems underlying a systematization of spectral data on the methanol molecule are formulated. Data on the energy levels and vacuum wavenumbers acquired from the published literature are presented in the form of information sources imported into the W@DIS information system. Sets of quantum numbers and labels used to describe the CH3OH molecular states are analyzed. The set of labels is different from universally accepted sets. A system of importing the data sources into W@DIS is outlined. The structure of databases characterizing transitions in an isolated CH3OH molecule is introduced and a digital library of the relevant published literature is discussed. A brief description is given of an imported data quality analysis and representation of the results obtained in the form of ontologies for subsequent computer processing.

Toward atomic resolution diffractive imaging of isolated molecules with x-ray free-electron lasers

DEFF Research Database (Denmark)

Stern, Stephan; Holmegaard, Lotte; Filsinger, Frank

2014-01-01

We give a detailed account of the theoretical analysis and the experimental results of an x-ray-diffraction experiment on quantum-state selected and strongly laser-aligned gas-phase ensembles of the prototypical large asymmetric rotor molecule 2,5-diiodobenzonitrile, performed at the Linac Cohere...

Interaction of slow electrons with high-pressure gases (Quasi-liquids). Synthesis of our knowledge on slow electron-molecule interactions. Progress report for year ending June 15, 1984

International Nuclear Information System (INIS)

McCorkle, D.L.; Christophorou, L.G.

1984-01-01

A crucial step in efforts to develop not only a coherent picture of radiation interaction with matter, but also to understand radiation effects and mechanisms, as well as the effects of chemical pollutants and toxic compounds, is to relate the often abundant knowledge on isolated molecules (low pressure gases) to that on liquids or solids. To understand the roles of the physical and chemical properties of molecules in biological reactions, the way these isolated-molecule properties change as molecules are embedded in gradually thicker and thicker (denser and denser) gaseous and, finally, liquid environments must be known. The work reported here, carried out both at the Physics Department of the University of Tennessee and at the Oak Ridge National Laboratory addresses itself to this question. At both places, high pressure (40 to approx. 8000 kPa) electron swarm experiments are currently in operation yielding the first information as to the effects of the density and nature of the environment on fundamental electron-molecule interaction processes at densities intermediate to those corresponding to low pressure gases and liquids, and the gradual transition from isolated molecule to condensed phase behavior. Basic physical data on the electronic states of atmospheric halocarbons in general, and of polycyclic aromatic hydrocarbons in particular were also studied. Such data are of special significance because of the occurrence of these molecules in the atmosphere, and are presently lacking

Enhanced polarizability of aromatic molecules placed in the vicinity of silver clusters

International Nuclear Information System (INIS)

Mayer, A; Schatz, G C

2009-01-01

We use a charge-dipole interaction model to study the polarizability of aromatic molecules that are placed between two silver clusters. In particular we examine the enhancement in polarizability induced by the clusters at plasmon-like resonant frequencies of the cluster-molecule-cluster system. The model used for these simulations relies on representation of the atoms by both a net electric charge and a dipole. By relating the time variation of the atomic charges to the currents that flow through the bonds of the structures considered, a least-action principle can be formulated that enables the atomic charges and dipoles to be determined. We consider benzene, naphthalene and anthracene for this study, comparing the polarizability of these aromatic molecules when placed in the middle between two Ag 120 clusters, with their polarizability as isolated molecules. We find that the polarizability of these molecules is enhanced by the clusters, and this increases the electromagnetic coupling between the two clusters. This results in significant red-shifting (by up to 0.8 eV) of the lowest energy optical transition in the cluster-molecule-cluster system compared to plasmon-like excitation in the cluster-cluster system. The resulting resonant polarizability enhancement leads to an electromagnetic enhancement in surface-enhanced Raman scattering of over 10 6 .

Cell factory-derived bioactive molecules with polymeric cryogel scaffold enhance the repair of subchondral cartilage defect in rabbits.

Science.gov (United States)

Gupta, Ankur; Bhat, Sumrita; Chaudhari, Bhushan P; Gupta, Kailash C; Tägil, Magnus; Zheng, Ming Hao; Kumar, Ashok; Lidgren, Lars

2017-06-01

We have explored the potential of cell factory-derived bioactive molecules, isolated from conditioned media of primary goat chondrocytes, for the repair of subchondral cartilage defects. Enzyme-linked immunosorbent assay (ELISA) confirms the presence of transforming growth factor-β1 in an isolated protein fraction (12.56 ± 1.15 ng/mg protein fraction). These bioactive molecules were used alone or with chitosan-agarose-gelatin cryogel scaffolds, with and without chondrocytes, to check whether combined approaches further enhance cartilage repair. To evaluate this, an in vivo study was conducted on New Zealand rabbits in which a subchondral defect (4.5 mm wide × 4.5 mm deep) was surgically created. Starting after the operation, bioactive molecules were injected at the defect site at regular intervals of 14 days. Histopathological analysis showed that rabbits treated with bioactive molecules alone had cartilage regeneration after 4 weeks. However, rabbits treated with bioactive molecules along with scaffolds, with or without cells, showed cartilage formation after 3 weeks; 6 weeks after surgery, the cartilage regenerated in rabbits treated with either bioactive molecules alone or in combinations showed morphological similarities to native cartilage. No systemic cytotoxicity or inflammatory response was induced by any of the treatments. Further, ELISA was done to determine systemic toxicity, which showed no difference in concentration of tumour necrosis factor-α in blood serum, before or after surgery. In conclusion, intra-articular injection with bioactive molecules alone may be used for the repair of subchondral cartilage defects, and bioactive molecules along with chondrocyte-seeded scaffolds further enhance the repair. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Reversible Guest Exchange Mechanisms in Supramolecular Host-GuestAssemblies

Energy Technology Data Exchange (ETDEWEB)

Pluth, Michael D.; Raymond, Kenneth N.

2006-09-01

Synthetic chemists have provided a wide array of supramolecular assemblies able to encapsulate guest molecules. The scope of this tutorial review focuses on supramolecular host molecules capable of reversibly encapsulating polyatomic guests. Much work has been done to determine the mechanism of guest encapsulation and guest release. This review covers common methods of monitoring and characterizing guest exchange such as NMR, UV-VIS, mass spectroscopy, electrochemistry, and calorimetry and also presents representative examples of guest exchange mechanisms. The guest exchange mechanisms of hemicarcerands, cucurbiturils, hydrogen-bonded assemblies, and metal-ligand assemblies are discussed. Special attention is given to systems which exhibit constrictive binding, a motif common in supramolecular guest exchange systems.

On the local theory of resonant inelastic collisions of slow electrons with carbon dioxide

International Nuclear Information System (INIS)

Kazansky, A.K.; Sergeeva, L.Yu.

1994-01-01

A method of calculating the cross sections of inelastic vibronic transitions in collisions of slow electrons with polyatomic molecules in the framework of the local theory (the 'boomerang' model) is proposed. The method is based on the study of the time evolution of the initial vibronic wavefunction; the evolution is governed by the (complex valued) Hamiltonian of the intermediate anion state. The method has been applied to the consideration of inelastic electron collisions with the CO 2 molecule in the two-mode approximation (symmetrical stretching and bending). The results obtained demonstrate the importance of the two-mode description for the system which can undergo the Renner transition. (Author)

Matrix isolation-infrared and mass spectrometric studies of high-temperature molecules

International Nuclear Information System (INIS)

Dickinson, S.

1987-08-01

Matrix isolation-infrared spectroscopy and mass spectrometry have been developed at AEE Winfrith to study the high-temperature vapour species which could be generated during a hypothetical severe reactor accident. The principles of the techniques and the instruments are described in detail, and examples of their application to specific systems discussed. Although these examples refer to high-temperature chemical species which are relevant to reactor safety assessments, the techniques are equally applicable to other processes where the characterisation of transient vapour-phase species is required. (author)

Astronomical chemistry.

Science.gov (United States)

Klemperer, William

2011-01-01

The discovery of polar polyatomic molecules in higher-density regions of the interstellar medium by means of their rotational emission detected by radioastronomy has changed our conception of the universe from essentially atomic to highly molecular. We discuss models for molecule formation, emphasizing the general lack of thermodynamic equilibrium. Detailed chemical kinetics is needed to understand molecule formation as well as destruction. Ion molecule reactions appear to be an important class for the generally low temperatures of the interstellar medium. The need for the intrinsically high-quality factor of rotational transitions to definitively pin down molecular emitters has been well established by radioastronomy. The observation of abundant molecular ions both positive and, as recently observed, negative provides benchmarks for chemical kinetic schemes. Of considerable importance in guiding our understanding of astronomical chemistry is the fact that the larger molecules (with more than five atoms) are all organic.

Growing interstellar molecules with ion-molecule reactions

International Nuclear Information System (INIS)

Bohme, D.K.

1989-01-01

Laboratory measurements of gas-phase ion-molecule reactions continue to provide important insights into the chemistry of molecular growth in interstellar environments. It is also true that the measurements are becoming more demanding as larger molecules capture our interest. While some of these measurements are motivated by current developments in chemical models of interstellar environments or by new molecular observations by astronomers, others explore novel chemistry which can lead to predictions of new interstellar molecules. Here the author views the results of some recent measurements, taken in the Ion Chemistry Laboratory at York University with the SIFT technique, which address some of the current needs of modellers and observers and which also provide some new fundamental insight into molecular growth, particularly when it occurs in the presence of large molecules such as PAH molecules which are now thought to have a major influence on the chemistry of interstellar environments in which they are present

Effects of thin films on inventory, permeation and re-emission of energetic hydrogen

International Nuclear Information System (INIS)

Ohyabu, N.; Nakamura, Y.; Nakahara, Y.; Livshits, A.; Alimov, V.; Busnyuk, A.; Notkin, M.; Samartsev, A.; Doroshin, A.

2000-01-01

A non-metallic coating thicker than the implantation depth may protect a metal against tritium retention and permeation. However, a thinner film has quite the opposite effect: a dramatic increase of permeation and retention, and a corresponding suppression of re-emission. In view of the benefits expected from particle control with a superpermeable membrane placed right inside the divertor, the behavior of a Nb sample was investigated in a plasma-membrane device having a graphite target. Even polyatomic carbide coating was found not to hinder hydrogen absorption and permeation. Polyatomic non-carbide C films effectively inhibits it, but the formation of such films depends on H and C fluxes, H energy and metal temperature. A durable isolation of suprathermal hydrogen with the superpermeable membrane was observed at a high enough ratio between H and C fluxes, and the effects of carbon were found to have a non-monotonic temperature dependence

Influence of sulfur-bearing polyatomic species on high precision measurements of Cu isotopic composition

Science.gov (United States)

Pribil, M.J.; Wanty, R.B.; Ridley, W.I.; Borrok, D.M.

2010-01-01

An increased interest in high precision Cu isotope ratio measurements using multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS) has developed recently for various natural geologic systems and environmental applications, these typically contain high concentrations of sulfur, particularly in the form of sulfate (SO42-) and sulfide (S). For example, Cu, Fe, and Zn concentrations in acid mine drainage (AMD) can range from 100??g/L to greater than 50mg/L with sulfur species concentrations reaching greater than 1000mg/L. Routine separation of Cu, Fe and Zn from AMD, Cu-sulfide minerals and other geological matrices usually incorporates single anion exchange resin column chromatography for metal separation. During chromatographic separation, variable breakthrough of SO42- during anion exchange resin column chromatography into the Cu fractions was observed as a function of the initial sulfur to Cu ratio, column properties, and the sample matrix. SO42- present in the Cu fraction can form a polyatomic 32S-14N-16O-1H species causing a direct mass interference with 63Cu and producing artificially light ??65Cu values. Here we report the extent of the mass interference caused by SO42- breakthrough when measuring ??65Cu on natural samples and NIST SRM 976 Cu isotope spiked with SO42- after both single anion column chromatography and double anion column chromatography. A set of five 100??g/L Cu SRM 976 samples spiked with 500mg/L SO42- resulted in an average ??65Cu of -3.50?????5.42??? following single anion column separation with variable SO42- breakthrough but an average concentration of 770??g/L. Following double anion column separation, the average SO42-concentration of 13??g/L resulted in better precision and accuracy for the measured ??65Cu value of 0.01?????0.02??? relative to the expected 0??? for SRM 976. We conclude that attention to SO42- breakthrough on sulfur-rich samples is necessary for accurate and precise measurements of ??65Cu and may require

Calix[4]arene Based Single-Molecule Magnets

Energy Technology Data Exchange (ETDEWEB)

Karotsis, Georgios; Teat, Simon J.; Wernsdorfer, Wolfgang; Piligkos, Stergios; Dalgarno, Scott J.; Brechin, Euan K.

2009-06-04

Single-molecule magnets (SMMs) have been the subject of much interest in recent years because their molecular nature and inherent physical properties allow the crossover between classical and quantum physics to be observed. The macroscopic observation of quantum phenomena - tunneling between different spin states, quantum interference between tunnel paths - not only allows scientists to study quantum mechanical laws in great detail, but also provides model systems with which to investigate the possible implementation of spin-based solid state qubits and molecular spintronics. The isolation of small, simple SMMs is therefore an exciting prospect. To date almost all SMMs have been made via the self-assembly of 3d metal ions in the presence of bridging/chelating organic ligands. However, very recently an exciting new class of SMMs, based on 3d metal clusters (or single lanthanide ions) housed within polyoxometalates, has appeared. These types of molecule, in which the SMM is completely encapsulated within (or shrouded by) a 'protective' organic or inorganic sheath have much potential for design and manipulation: for example, for the removal of unwanted dipolar interactions, the introduction of redox activity, or to simply aid functionalization for surface grafting. Calix[4]arenes are cyclic (typically bowl-shaped) polyphenols that have been used extensively in the formation of versatile self-assembled supramolecular structures. Although many have been reported, p-{sup t}But-calix[4]arene and calix[4]arene (TBC4 and C4 respectively, Figure 1A) are frequently encountered due to (a) synthetic accessibility, and (b) vast potential for alteration at either the upper or lower rim of the macrocyclic framework. Within the field of supramolecular chemistry, TBC4 is well known for interesting polymorphic behavior and phase transformations within anti-parallel bi-layer arrays, while C4 often forms self-included trimers. The polyphenolic nature of calix[n]arenes (where

Molecule nanoweaver

Science.gov (United States)

Gerald, II; Rex, E [Brookfield, IL; Klingler, Robert J [Glenview, IL; Rathke, Jerome W [Homer Glen, IL; Diaz, Rocio [Chicago, IL; Vukovic, Lela [Westchester, IL

2009-03-10

A method, apparatus, and system for constructing uniform macroscopic films with tailored geometric assemblies of molecules on the nanometer scale. The method, apparatus, and system include providing starting molecules of selected character, applying one or more force fields to the molecules to cause them to order and condense with NMR spectra and images being used to monitor progress in creating the desired geometrical assembly and functionality of molecules that comprise the films.

Isolation of Synaptosomes, Synaptic Plasma Membranes, and Synaptic Junctional Complexes.

Science.gov (United States)

Michaelis, Mary L; Jiang, Lei; Michaelis, Elias K

2017-01-01

Isolation of synaptic nerve terminals or synaptosomes provides an opportunity to study the process of neurotransmission at many levels and with a variety of approaches. For example, structural features of the synaptic terminals and the organelles within them, such as synaptic vesicles and mitochondria, have been elucidated with electron microscopy. The postsynaptic membranes are joined to the presynaptic "active zone" of transmitter release through cell adhesion molecules and remain attached throughout the isolation of synaptosomes. These "post synaptic densities" or "PSDs" contain the receptors for the transmitters released from the nerve terminals and can easily be seen with electron microscopy. Biochemical and cell biological studies with synaptosomes have revealed which proteins and lipids are most actively involved in synaptic release of neurotransmitters. The functional properties of the nerve terminals, such as responses to depolarization and the uptake or release of signaling molecules, have also been characterized through the use of fluorescent dyes, tagged transmitters, and transporter substrates. In addition, isolated synaptosomes can serve as the starting material for the isolation of relatively pure synaptic plasma membranes (SPMs) that are devoid of organelles from the internal environment of the nerve terminal, such as mitochondria and synaptic vesicles. The isolated SPMs can reseal and form vesicular structures in which transport of ions such as sodium and calcium, as well as solutes such as neurotransmitters can be studied. The PSDs also remain associated with the presynaptic membranes during isolation of SPM fractions, making it possible to isolate the synaptic junctional complexes (SJCs) devoid of the rest of the plasma membranes of the nerve terminals and postsynaptic membrane components. Isolated SJCs can be used to identify the proteins that constitute this highly specialized region of neurons. In this chapter, we describe the steps involved

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

Science.gov (United States)

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

2009-03-01

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

Absolute configurations of zingiberenols isolated from ginger (Zingiber officinale) rhizomes

Science.gov (United States)

The sesquiterpene alcohol zingiberenol, or 1,10-bisaboladien-3-ol, was isolated some time ago from ginger, Zingiber officinale, rhizomes, but its absolute configuration had not been determined. With three chiral centers present in the molecule, zingiberenol can exist in eight stereoisomeric forms. ...

Snake Venom PLA2s Inhibitors Isolated from Brazilian Plants: Synthetic and Natural Molecules

Science.gov (United States)

Carvalho, B. M. A.; Santos, J. D. L.; Xavier, B. M.; Almeida, J. R.; Resende, L. M.; Martins, W.; Marcussi, S.; Marangoni, S.; Stábeli, R. G.; Calderon, L. A.; Soares, A. M.; Da Silva, S. L.; Marchi-Salvador, D. P.

2013-01-01

Ophidian envenomation is an important health problem in Brazil and other South American countries. In folk medicine, especially in developing countries, several vegetal species are employed for the treatment of snakebites in communities that lack prompt access to serum therapy. However, the identification and characterization of the effects of several new plants or their isolated compounds, which are able to inhibit the activities of snake venom, are extremely important and such studies are imperative. Snake venom contains several organic and inorganic compounds; phospholipases A2 (PLA2s) are one of the principal toxic components of venom. PLA2s display a wide variety of pharmacological activities, such as neurotoxicity, myotoxicity, cardiotoxicity, anticoagulant, hemorrhagic, and edema-inducing effects. PLA2 inhibition is of pharmacological and therapeutic interests as these enzymes are involved in several inflammatory diseases. This review describes the results of several studies of plant extracts and their isolated active principles, when used against crude snake venoms or their toxic fractions. Isolated inhibitors, such as steroids, terpenoids, and phenolic compounds, are able to inhibit PLA2s from different snake venoms. The design of specific inhibitors of PLA2s might help in the development of new pharmaceutical drugs, more specific antivenom, or even as alternative approaches for treating snakebites. PMID:24171158

Snake Venom PLA2s Inhibitors Isolated from Brazilian Plants: Synthetic and Natural Molecules

Directory of Open Access Journals (Sweden)

B. M. A. Carvalho

2013-01-01

Full Text Available Ophidian envenomation is an important health problem in Brazil and other South American countries. In folk medicine, especially in developing countries, several vegetal species are employed for the treatment of snakebites in communities that lack prompt access to serum therapy. However, the identification and characterization of the effects of several new plants or their isolated compounds, which are able to inhibit the activities of snake venom, are extremely important and such studies are imperative. Snake venom contains several organic and inorganic compounds; phospholipases A2 (PLA2s are one of the principal toxic components of venom. PLA2s display a wide variety of pharmacological activities, such as neurotoxicity, myotoxicity, cardiotoxicity, anticoagulant, hemorrhagic, and edema-inducing effects. PLA2 inhibition is of pharmacological and therapeutic interests as these enzymes are involved in several inflammatory diseases. This review describes the results of several studies of plant extracts and their isolated active principles, when used against crude snake venoms or their toxic fractions. Isolated inhibitors, such as steroids, terpenoids, and phenolic compounds, are able to inhibit PLA2s from different snake venoms. The design of specific inhibitors of PLA2s might help in the development of new pharmaceutical drugs, more specific antivenom, or even as alternative approaches for treating snakebites.

Spectroscopy of Cold LiCa Molecules Formed on Helium Nanodroplets

Science.gov (United States)

2013-01-01

We report on the formation of mixed alkali–alkaline earth molecules (LiCa) on helium nanodroplets and present a comprehensive experimental and theoretical study of the ground and excited states of LiCa. Resonance enhanced multiphoton ionization time-of-flight (REMPI-TOF) spectroscopy and laser induced fluorescence (LIF) spectroscopy were used for the experimental investigation of LiCa from 15000 to 25500 cm–1. The 42Σ+ and 32Π states show a vibrational structure accompanied by distinct phonon wings, which allows us to determine molecular parameters as well as to study the interaction of the molecule with the helium droplet. Higher excited states (42Π, 52Σ+, 52Π, and 62Σ+) are not vibrationally resolved and vibronic transitions start to overlap. The experimental spectrum is well reproduced by high-level ab initio calculations. By using a multireference configuration interaction (MRCI) approach, we calculated the 19 lowest lying potential energy curves (PECs) of the LiCa molecule. On the basis of these calculations, we could identify previously unobserved transitions. Our results demonstrate that the helium droplet isolation approach is a powerful method for the characterization of tailor-made alkali–alkaline earth molecules. In this way, important contributions can be made to the search for optimal pathways toward the creation of ultracold alkali–alkaline earth ground state molecules from the corresponding atomic species. Furthermore, a test for PECs calculated by ab initio methods is provided. PMID:24028555

Nanotubule and Tour Molecule Based Molecular Electronics: Suggestion for a Hybrid Approach

Science.gov (United States)

Srivastava, Deepak; Saini, Subhash (Technical Monitor)

1998-01-01

Recent experimental and theoretical attempts and results indicate two distinct broad pathways towards future molecular electronic devices and architectures. The first is the approach via Tour type ladder molecules and their junctions which can be fabricated with solution phase chemical approaches. Second are fullerenes or nanotubules and their junctions which may have better conductance, switching and amplifying characteristics but can not be made through well controlled and defined chemical means. A hybrid approach combining the two pathways to take advantage of the characteristics of both is suggested. Dimension and scale of such devices would be somewhere in between isolated molecule and nanotubule based devices but it maybe possible to use self-assembly towards larger functional and logicalunits.

A Review Study on Macrolides Isolated from Cyanobacteria.

Science.gov (United States)

Wang, Mengchuan; Zhang, Jinrong; He, Shan; Yan, Xiaojun

2017-04-26

Cyanobacteria are rich sources of structurally-diverse molecules with promising pharmacological activities. Marine cyanobacteria have been proven to be true producers of some significant bioactive metabolites from marine invertebrates. Macrolides are a class of bioactive compounds isolated from marine organisms, including marine microorganisms in particular. The structural characteristics of macrolides from cyanobacteria mainly manifest in the diversity of carbon skeletons, complexes of chlorinated thiazole-containing molecules and complex spatial configuration. In the present work, we systematically reviewed the structures and pharmacological activities of macrolides from cyanobacteria. Our data would help establish an effective support system for the discovery and development of cyanobacterium-derived macrolides.

Consistent force field modeling of matrix isolated molecules. V. Minimum energy path potential to the conformer conversion of 1,2-difluoroethane: Ar 364, ab initio calculation of electric multipole moments and electric polarization contribution to the conversion barrier

Science.gov (United States)

Gunde, R.; Ha, T.-K.; Günthard, H. H.

1990-08-01

In this paper results of consistent force field modeling (CFF) of the potential function to conversion of the gauche (g) to the trans (t) conformer of 1,2-difluoroethane (DFE) isolated in an argon matrix will be reported. Starting point are locally stable configurations gDFE:Ar 364 (defect GH1) and tDFE:Ar 364 (TH1) obtained in previous work from CFF modeling of a cube shaped Ar 364 fragment containing one DFE molecule in its center. Using the dihedral angle of DFE as an independent parameter the minimum energy path of the conversion process gDFE:Ar 364→tDFE:Ar 364 will be determined by CFF energy minimization. Determination of the minimum energy path is found to require large numbers of energy minimization steps and to lead to a rather complicated motion of the molecule with respect to the crystal fragment. Surprisingly the molecule-matrix interactions lead to a reduction of the g-t barrier by ≈500 cal/mol and to a stabilization of the trans species by ≈500 cal/mol. This finding is a consequence of a delicate interplay of matrix-molecule and matrix-matrix interactions. Calculation of the electric polarization energy (induced dipole-first-order polarization approximation) is based on extended ab initio calculations of dipole and quadrupole moments and a bond polarizability estimate of the first-order polarizability of DFE as a function of the internal rotation angle, on Fourier expansion of multipole components and use of symmetry for reduction of the order of the linear system defining the (self-consistent) induced dipole moments of all Ar atoms. Electric polarization is found to alter the potential function of the conversion process in a profound way: the g-t barrier and the t-g energy difference are increased to ≈3000 cal/mol and to ≈1500 cal/mol respectively (≈2500 and ≈530 cal/mol respectively for free DFE). Further applications of the technique developed in this work to related problems of matrix isolated molecules, e.g., vibrational matrix

Isolation, Synthesis, and Antisepsis Effects of a C-Methylcoumarinochromone Isolated from Abronia nana Cell Culture.

Science.gov (United States)

Lee, Wonhwa; Lee, Doohyun; Lee, Yuri; Lee, Taeho; Song, Kyung-Sik; Yang, Eun-Ju; Bae, Jong-Sup

2018-05-25

Only a few isoflavones have been isolated from plants of the genus Abronia. The biological properties of compounds isolated from Abronia species have not been well established, and their antisepsis effects have not been reported yet. In the present study, a new C-methylcoumarinochromone, was isolated from Abronia nana suspension cultures. Its structure was deduced as 9,11-dihydroxy-10-methylcoumarinochromone (boeravinone Y, 1) by spectroscopic data analysis and verified by chemical synthesis. The potential inhibitory effects of 1 against high mobility group box 1 (HMGB1)-mediated septic responses were investigated. Results showed that 1 effectively inhibited lipopolysaccharide-induced release of HMGB1 and suppressed HMGB1-mediated septic responses, in terms of reduction of hyperpermeability, leukocyte adhesion and migration, and cell adhesion molecule expression. In addition, 1 increased the phagocytic activity of macrophages and exhibited bacterial clearance effects in the peritoneal fluid and blood of mice with cecal ligation and puncture-induced sepsis. Collectively, these results suggested that 1 might have potential therapeutic activity against various severe vascular inflammatory diseases via inhibition of the HMGB1 signaling pathway.

Calculating constants of the rates of the reactions of excitation, ionization, and atomic exchange: A model of a shock oscillator with a change of the Hamiltonian of the system

Science.gov (United States)

Tsyganov, D. L.

2017-11-01

A new model for calculating the rates of reactions of excitation, ionization, and atomic exchange is proposed. Diatomic molecule AB is an unstructured particle M upon the exchange of elastic-vibrational (VT) energy, i.e., a model of a shock forceful oscillator with a change in Hamiltonian (SFOH). The SFOH model is based on the quantum theory of strong perturbations. The SFOH model allows generalization in simulating the rates of the reactions of excitation, ionization, and atomic exchange in the vibrational-vibrational (VV) energy exchange of diatomic molecules, and the exchange of VV- and VT-energy of polyatomic molecules. The rate constants of the excitation of metastables A 3Σ u +, B 3Π g , W 3Δ u , B'3Σ u -, a'3Σ u -, and the ionization of a nitrogen molecules from ground state X2Σ g + upon a collision with a heavy structureless particle (a nitrogen molecule), are found as examples.

Effects of sub-culturing on genetic and physiological parameters in different Beauveria bassiana isolates.

Science.gov (United States)

Eivazian Kary, Naser; Alizadeh, Zhila

2017-05-01

Beauveria bassiana is a fungus which is widely used as a biological insecticide to control a number of economically important insect pests. Knowledge of the genetic diversity of the isolates, understanding the underlying nature of these evolutionary phenomena and finding appropriate and simple screening tools play an important role in developing effective biocontrol agents. Here, we monitored changes of electrophoretic karyotype of small molecules of extrachromosomal DNAs, presumably mitochondrial DNA or plasmids in several individual isolates of B. bassiana during the forced in vitro evolution by continual subculture on artificial media and then we evaluated these changes on the virulence of the isolates. Through agarose gel electrophoresis of the small extrachromosomal DNAs molecules, we found that mutations accumulate quickly and obvious changes take place in extrachromosomal DNAs of some isolates, although this did not always occur. This plasticity in response to culturing pressure suggests that buffering capacity of fungal genome against mutations is isolate dependent. Following the forced evolution by sub-culturing, five discriminable electrophoretic karyotype of extrachromosomal DNAs was observed among isolates. The results showed that some isolates are prone to deep mutations, but during enforced sub-culturing some others have efficiently conserved genome. These differences are influensive in screening appropriate isolates for mass production as a keystone in biocontrol program. To determine the effects of these changes on isolate traits, virulence, germination rate and spore-bound Pr1 activity were assessed parallel to sub-culturing. The results clearly revealed that parallel to sub-culturing and in correlation with karyotypic changes, isolates significantly suffered from virulence, germination rate and spore-bound Pr1 activity deficiencies. Copyright © 2017 Elsevier Inc. All rights reserved.

Single-molecule magnets ``without'' intermolecular interactions

Science.gov (United States)

Wernsdorfer, W.; Vergnani, L.; Rodriguez-Douton, M. J.; Cornia, A.; Neugebauer, P.; Barra, A. L.; Sorace, L.; Sessoli, R.

2012-02-01

Intermolecular magnetic interactions (dipole-dipole and exchange) affect strongly the magnetic relaxation of crystals of single-molecule magnets (SMMs), especially at low temperature, where quantum tunneling of the magnetization (QTM) dominates. This leads to complex many-body problems [l]. Measurements on magnetically diluted samples are desirable to clearly sort out the behaviour of magnetically-isolated SMMs and to reveal, by comparison, the effect of intermolecular interactions. Here, we diluted a Fe4 SMM into a diamagnetic crystal lattice, affording arrays of independent and iso-oriented magnetic units. We found that the resonant tunnel transitions are much sharper, the tunneling efficiency changes significantly, and two-body QTM transitions disappear. These changes have been rationalized on the basis of a dipolar shuffling mechanism and of transverse dipolar fields, whose effect has been analyzed using a multispin model. Our findings directly prove the impact of intermolecular magnetic couplings on the SMM behaviour and disclose the magnetic response of truly-isolated giant spins in a diamagnetic crystalline environment.[4pt] [1] W. Wernsdorfer, at al, PRL 82, 3903 (1999); PRL 89, 197201 (2002); Nature 416, 406 (2002); IS Tupitsyn, PCE Stamp, NV Prokof'ev, PRB 69, 132406 (2004).

Applications of a simple dynamical model to the reaction path Hamiltonian: tunneling corrections to rate constants, product state distributions, line widths of local mode overtones, and mode specificity in unimolecular decomposition

International Nuclear Information System (INIS)

Cerjan, C.J.; Shi, S.; Miller, W.H.

1982-01-01

A simple but often reasonably accurate dynamical model--a synthesis of the semiclassical perturbation (SCP) approximation of Miller and Smith and the infinite order sudden (IOS) approximation--has been shown previously to take an exceptionally simple form when applied to the reaction path Hamiltonian derived by Miller, Handy, and Adams. This paper shows how this combined SCP-IOS reaction path model can be used to provide a simple but comprehensive description of a variety of phenomena in the dynamics of polyatomic molecules

Identification of potential local isolated for biosurfactant production

Science.gov (United States)

Shafiei, Zahra; Yusoff, Wan Mohtar Wan; Hamid, Aidil Abdul; Moazami, Nasrin; Hamzah, Ainon; Fooladi, Taybeh

2013-11-01

Biosurfactant are amphiphilic molecule that have received increasing attention in recent years because of their role in the growth of microorganisms on water-insoluble hydrophobic materials such as hydrocarbons as well as their commercial potential in the cosmetics, food, oil recovery and agricultural industries. In this study a potential biosurfactant producing strain was isolated from several soil samples of Terengganu oil refinery, Malaysia and selected during preliminary screening using hemolytic activity, oil spreading and drop collapsed technique. Isolates with at least more than one positive response to these three methods were subjected to complementary screening by measuring surface tension reduction as well as emulsification capacity. The biosurfactant produced by isolated 5M was able to reduced surface tension of culture medium from 60 mN/m to30mN/m. The biochemical and morphological characterization, 16SrRNA gene sequencing showed that the isolated 5M belongs to bacillus groups. The maximum production of biosurfactant by Bacillus 5M was observed after 48 h of incubation.

Isolation of Biosurfactant Producing Bacteria from Oil Reservoirs

Directory of Open Access Journals (Sweden)

A Tabatabaee, M Mazaheri Assadi, AA Noohi,VA Sajadian

2005-01-01

Full Text Available Biosurfactants or surface-active compounds are produced by microoaganisms. These molecules reduce surface tension both aqueous solutions and hydrocarbon mixtures. In this study, isolation and identification of biosurfactant producing bacteria were assessed. The potential application of these bacteria in petroleum industry was investigated. Samples (crude oil were collected from oil wells and 45 strains were isolated. To confirm the ability of isolates in biosurfactant production, haemolysis test, emulsification test and measurement of surface tension were conducted. We also evaluated the effect of different pH, salinity concentrations, and temperatures on biosurfactant production. Among importance features of the isolated strains, one of the strains (NO.4: Bacillus.sp showed high salt tolerance and their successful production of biosurfactant in a vast pH and temperature domain and reduced surface tension to value below 40 mN/m. This strain is potential candidate for microbial enhanced oil recovery. The strain4 biosurfactant component was mainly glycolipid in nature.

Simple test system for single molecule recognition force microscopy

International Nuclear Information System (INIS)

Riener, Christian K.; Stroh, Cordula M.; Ebner, Andreas; Klampfl, Christian; Gall, Alex A.; Romanin, Christoph; Lyubchenko, Yuri L.; Hinterdorfer, Peter; Gruber, Hermann J.

2003-01-01

We have established an easy-to-use test system for detecting receptor-ligand interactions on the single molecule level using atomic force microscopy (AFM). For this, avidin-biotin, probably the best characterized receptor-ligand pair, was chosen. AFM sensors were prepared containing tethered biotin molecules at sufficiently low surface concentrations appropriate for single molecule studies. A biotin tether, consisting of a 6 nm poly(ethylene glycol) (PEG) chain and a functional succinimide group at the other end, was newly synthesized and covalently coupled to amine-functionalized AFM tips. In particular, PEG 800 diamine was glutarylated, the mono-adduct NH 2 -PEG-COOH was isolated by ion exchange chromatography and reacted with biotin succinimidylester to give biotin-PEG-COOH which was then activated as N-hydroxysuccinimide (NHS) ester to give the biotin-PEG-NHS conjugate which was coupled to the aminofunctionalized AFM tip. The motional freedom provided by PEG allows for free rotation of the biotin molecule on the AFM sensor and for specific binding to avidin which had been adsorbed to mica surfaces via electrostatic interactions. Specific avidin-biotin recognition events were discriminated from nonspecific tip-mica adhesion by their typical unbinding force (∼40 pN at 1.4 nN/s loading rate), unbinding length (<13 nm), the characteristic nonlinear force-distance relation of the PEG linker, and by specific block with excess of free d-biotin. The convenience of the test system allowed to evaluate, and compare, different methods and conditions of tip aminofunctionalization with respect to specific binding and nonspecific adhesion. It is concluded that this system is well suited as calibration or start-up kit for single molecule recognition force microscopy

Solid state {sup 1}H spin-lattice relaxation and isolated-molecule and cluster electronic structure calculations in organic molecular solids: The relationship between structure and methyl group and t-butyl group rotation

Energy Technology Data Exchange (ETDEWEB)

Wang, Xianlong, E-mail: WangXianlong@uestc.edu.cn, E-mail: pbeckman@brynmawr.edu [Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, 4 North Jianshe Rd., 2nd Section, Chengdu 610054 (China); Mallory, Frank B. [Department of Chemistry, Bryn Mawr College, 101 North Merion Ave., Bryn Mawr, Pennsylvania 19010-2899 (United States); Mallory, Clelia W. [Department of Chemistry, Bryn Mawr College, 101 North Merion Ave., Bryn Mawr, Pennsylvania 19010-2899 (United States); Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323 (United States); Odhner, Hosanna R.; Beckmann, Peter A., E-mail: WangXianlong@uestc.edu.cn, E-mail: pbeckman@brynmawr.edu [Department of Physics, Bryn Mawr College, 101 North Merion Ave., Bryn Mawr, Pennsylvania 19010-2899 (United States)

2014-05-21

We report ab initio density functional theory electronic structure calculations of rotational barriers for t-butyl groups and their constituent methyl groups both in the isolated molecules and in central molecules in clusters built from the X-ray structure in four t-butyl aromatic compounds. The X-ray structures have been reported previously. We also report and interpret the temperature dependence of the solid state {sup 1}H nuclear magnetic resonance spin-lattice relaxation rate at 8.50, 22.5, and 53.0 MHz in one of the four compounds. Such experiments for the other three have been reported previously. We compare the computed barriers for methyl group and t-butyl group rotation in a central target molecule in the cluster with the activation energies determined from fitting the {sup 1}H NMR spin-lattice relaxation data. We formulate a dynamical model for the superposition of t-butyl group rotation and the rotation of the t-butyl group's constituent methyl groups. The four compounds are 2,7-di-t-butylpyrene, 1,4-di-t-butylbenzene, 2,6-di-t-butylnaphthalene, and 3-t-butylchrysene. We comment on the unusual ground state orientation of the t-butyl groups in the crystal of the pyrene and we comment on the unusually high rotational barrier of these t-butyl groups.

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

Science.gov (United States)

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

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

Rhodotorula mucilaginosa, a quorum quenching yeast exhibiting lactonase activity isolated from a tropical shoreline.

Science.gov (United States)

Ghani, Norshazliza Ab; Sulaiman, Joanita; Ismail, Zahidah; Chan, Xin-Yue; Yin, Wai-Fong; Chan, Kok-Gan

2014-04-09

Two microbial isolates from a Malaysian shoreline were found to be capable of degrading N-acylhomoserine lactones. Both Matrix Assisted Laser Desorption Ionization-Time of Flight-Mass Spectrometry and 18S rDNA phylogenetic analyses confirmed that these isolates are Rhodotorula mucilaginosa. Quorum quenching activities were detected by a series of bioassays and rapid resolution liquid chromatography analysis. The isolates were able to degrade various quorum sensing molecules namely N-hexanoyl-L-homoserine lactone (C6-HSL), N-(3-oxo-hexanoyl)-L-homoserine lactone (3-oxo-C6-HSL) and N-(3-hydroxyhexanoyl)-L-homoserine lactone (3-hydroxy-C6-HSL). Using a relactonisation assay to verify the quorum quenching mechanism, it is confirmed that Rh. mucilaginosa degrades the quorum sensing molecules via lactonase activity. To the best of our knowledge, this is the first documentation of the fact that Rh. mucilaginosa has activity against a broad range of AHLs namely C6-HSL, 3-oxo-C6-HSL and 3-hydroxy-C6-HSL.

Effect of Skimmer Cone Material on the Spectra of Inductively Coupled Plasma Mass Spectrometry

International Nuclear Information System (INIS)

Amr, M.A.; Zahran, N.F.; Helal, A.I.

2002-01-01

The inductively coupled plasma ion source for mass spectrometry is very sensitive for multielement analysis with detection limits down to sub part per trillion (ppt). Polyatomic ions which could be formed in the mass spectra may interfere in the analysis of some element. Experimental conditions have great influences on the formation of polyatomic ions. The present work demonstrates that the skimmer materials (Au, Ag, Ni, and Cu) are participating in the formation of polyatomic ions, meanwhile the sampler materials have no real effect. The mechanism of formation of polyatomic ions is explained. Heats of formation of polyatomic species formed from the skimmer materials such as: Au X, Ag X, Ni X and Cu X; where X= Ar, O, N, C and H are calculated by Gaussian program (G 94 W)

Life's First Handshake - Discovery of the Interstellar Chiral Molecule Propylene Oxide

Science.gov (United States)

McGuire, Brett A.; Carroll, P. Brandon; Loomis, Ryan A.; Finneran, Ian A.; Jewell, Philip R.; Remijan, Anthony J.; Blake, Geoffrey A.

2016-06-01

Life on Earth relies on chiral molecules, that is, species not superimposable on their mirror images. This manifests itself in the selection of a single molecular handedness, or homochirality, across the biosphere, and is perhaps most readily apparent in the large enhancement in biological activity of particular amino acid and sugar enantiomers. Yet, the ancestral origin of biological homochirality remains a mystery. The non-racemic ratios in some organics isolated from primitive meteorites hint at a primordial chiral seed, but even these samples have experienced substantial processing during planetary assembly, obscuring their complete histories. To determine the underlying origin of any enantiomeric excess, it is critical to understand the molecular gas from which these molecules originated. Here, we present the first extra-solar, astronomical detection of a chiral molecule, propylene oxide (CH3CHCH2O), in absorption toward the Galactic Center. We discuss the implications of the detection on observational searches to determine a primordial chiral excess, as well as the state of laboratory efforts in these areas.

Imaging a multidimensional multichannel potential energy surface: Photodetachment of H(-)(NH3) and NH4 (.).

Science.gov (United States)

Hu, Qichi; Song, Hongwei; Johnson, Christopher J; Li, Jun; Guo, Hua; Continetti, Robert E

2016-06-28

Probes of the Born-Oppenheimer potential energy surfaces governing polyatomic molecules often rely on spectroscopy for the bound regions or collision experiments in the continuum. A combined spectroscopic and half-collision approach to image nuclear dynamics in a multidimensional and multichannel system is reported here. The Rydberg radical NH4 and the double Rydberg anion NH4 (-) represent a polyatomic system for benchmarking electronic structure and nine-dimensional quantum dynamics calculations. Photodetachment of the H(-)(NH3) ion-dipole complex and the NH4 (-) DRA probes different regions on the neutral NH4 PES. Photoelectron energy and angular distributions at photon energies of 1.17, 1.60, and 2.33 eV compare well with quantum dynamics. Photoelectron-photofragment coincidence experiments indicate dissociation of the nascent NH4 Rydberg radical occurs to H + NH3 with a peak kinetic energy of 0.13 eV, showing the ground state of NH4 to be unstable, decaying by tunneling-induced dissociation on a time scale beyond the present scope of multidimensional quantum dynamics.

Applications of Engineered DNA-Binding Molecules Such as TAL Proteins and the CRISPR/Cas System in Biology Research

Directory of Open Access Journals (Sweden)

Toshitsugu Fujita

2015-09-01

Full Text Available Engineered DNA-binding molecules such as transcription activator-like effector (TAL or TALE proteins and the clustered regularly interspaced short palindromic repeats (CRISPR and CRISPR-associated proteins (Cas (CRISPR/Cas system have been used extensively for genome editing in cells of various types and species. The sequence-specific DNA-binding activities of these engineered DNA-binding molecules can also be utilized for other purposes, such as transcriptional activation, transcriptional repression, chromatin modification, visualization of genomic regions, and isolation of chromatin in a locus-specific manner. In this review, we describe applications of these engineered DNA-binding molecules for biological purposes other than genome editing.

Antioxidant Potential of Cyclopeptyide Alkaloids Isolated from Zizyphus Oxphylla

International Nuclear Information System (INIS)

Kaleem, W.A.; Muhammad, N.; Khan, H.; Rauf, A.; Haq, M.Z.U.; Qayum, M.; Khan, A.Z.; Nisar, M.; Obaidullah, M.

2015-01-01

The present study reports on the antioxidant potential of five cyclopeptide alkaloids isolated from Zizyphus oxyphylla including Oxyphylline-D 1, Nummularin-C 2, Nummularin-R 3, Oxyphylline-B 4, Oxyphylline C 5 using DPPH free radical assay, nitric oxide radical assay and reducing power assay. The isolated alkaloids demonstrated marked antioxidant potential in a concentration dependent manner. Among the tested molecules, the compounds, 2 was most potent with IC50 values of 27.23, 32.03 and 22.45 μg/ml in DPPH free radical assay, nitric oxide radical assay and reducing power assay respectively. (author)

Palmitoylethanolamide (PEA)—‘Promiscuous’ anti-inflammatory and analgesic molecule at the interface between nutrition and pharma

NARCIS (Netherlands)

Keppel Hesselink, J.M.; Kopsky, D.J.; Witkamp, R.F.

2014-01-01

Palmitoylethanolamide (N-palmitoylethanolamine or PEA) is an endogenous fatty acid amide belonging to the N-acylethanolamine (NAE) class of signalling molecules. Earliest reports on the anti-inflammatory and immune modulating properties of PEA date back to 1957 when its isolation from soy lecithin,

Atkins' molecules

CERN Document Server

Atkins, Peters

2003-01-01

Originally published in 2003, this is the second edition of a title that was called 'the most beautiful chemistry book ever written'. In it, we see the molecules responsible for the experiences of our everyday life - including fabrics, drugs, plastics, explosives, detergents, fragrances, tastes, and sex. With engaging prose Peter Atkins gives a non-technical account of an incredible range of aspects of the world around us, showing unexpected connections, and giving an insight into how this amazing world can be understood in terms of the atoms and molecules from which it is built. The second edition includes dozens of extra molecules, graphical presentation, and an even more accessible and enthralling account of the molecules themselves.

Electronic relaxation processes in polyatomic molecules. Progress report, October 1, 1975--September 30, 1976

International Nuclear Information System (INIS)

Lim, E.C.

1976-09-01

Excitation energy dependence of radiationless decay rate under collision-free conditions was utilized as a probe of intramolecular vibrational relaxation in tetracene and pentacene. The results give evidence of vibrational relaxation which competes with electronic relaxation. The substitution dependence of T 1 (nπ*) → S 0 radiationless transition in monocyclic diazines and the temperature dependence of S 1 non-radiative decay rate in alcoholic solutions of polycyclic monoazines indicate that the vibronic interaction between the lowest energy nπ* and ππ* states leads to a rapid radiationless deactivation of the lower of the two electronic states. Finally, a photon-counting spectrofluorometer of very high sensitivity was constructed, and it was used to record T 2 → T 1 fluorescence in bromoanthracenes and S 2 → S 1 fluorescence in azulene. These spectra represent the first bona-fide, or the most convincing, observation of fluorescence between excited electronic states

Theoretical investigation of the ultrafast dissociation of core-ionized water and uracil molecules immersed in liquid water

Energy Technology Data Exchange (ETDEWEB)

Stia, C.R.; Fojon, O.A. [Instituto de Fisica Rosario - CONICET-Universidad Nacional de Rosario, Rosario (Argentina); Gaigeot, M.P. [Laboratoire Analyse et Modelisation pour la Biologie et l' Environnement, LAMBE, UMR-CNRS 8587, Universite d' Evry-Val-d' Essonne, 91 - Evry (France); Institut Universitaire de France, 75 - Paris (France); Vuilleumier, R. [Departement de chimie, Ecole Normale Superieure, 75 - Paris (France); Herve du Penhoat, M.A.; Politis, M.F. [Institut de Mineralogie et de Physique des Milieux Condenses, IMPMC, UMR-CNRS 7590, Universite Pierre et Marie Curie, 75 - Paris (France)

2010-10-15

We present a series of ab initio density functional based calculations of the fragmentation dynamics of core-ionized biomolecules. The computations are performed for pure liquid water, aqueous and isolated Uracil. Core ionization is described by replacing the 1s{sup 2} pseudopotential of one atom of the target molecule (C, N or O) with a pseudopotential for a 1s{sup 1} core-hole state. Our results predict that the dissociation of core-ionized water molecules may be reached during the lifetime of inner-shell vacancy (less than 10 fs), leading to OH bond breakage as a primary outcome. We also observe a second fragmentation channel in which total Coulomb explosion of the ionized water molecule occurs. Fragmentation pathways are found similar for pure water or when the water molecule is in the primary hydration shell of the uracil molecule. In the latter case, the proton may be transferred towards the uracil oxygen atoms. When the core hole is located on the uracil molecule, ultrafast dissociation is only observed in the aqueous environment and for nitrogen-K vacancies, resulting in proton transfers towards the hydrogen-bonded water molecule. (authors)

Cold Rydberg molecules

Science.gov (United States)

Raithel, Georg; Zhao, Jianming

2017-04-01

Cold atomic systems have opened new frontiers at the interface of atomic and molecular physics. These include research on novel types of Rydberg molecules. Three types of molecules will be reviewed. Long-range, homonuclear Rydberg molecules, first predicted in [1] and observed in [2], are formed via low-energy electron scattering of the Rydberg electron from a ground-state atom within the Rydberg atom's volume. The binding mostly arises from S- and P-wave triplet scattering. We use a Fermi model that includes S-wave and P-wave singlet and triplet scattering, the fine structure coupling of the Rydberg atom and the hyperfine structure coupling of the 5S1/2 atom (in rubidium [3]). The hyperfine structure gives rise to mixed singlet-triplet potentials for both low-L and high-L Rydberg molecules [3]. A classification into Hund's cases [3, 4, 5] will be discussed. The talk further includes results on adiabatic potentials and adiabatic states of Rydberg-Rydberg molecules in Rb and Cs. These molecules, which have even larger bonding length than Rydberg-ground molecules, are formed via electrostatic multipole interactions. The leading interaction term of neutral Rydberg-Rydberg molecules is between two dipoles, while for ionic Rydberg molecules it is between a dipole and a monopole. NSF (PHY-1506093), NNSF of China (61475123).

Production of N-acyl-L-homoserine lactones by P. aeruginosa isolates from chronic lung infections associated with cystic fibrosis

DEFF Research Database (Denmark)

Geisenberger, O; Givskov, M; Riedel, K

2000-01-01

The N-acyl-L-homoserine lactones (AHLs) produced by sequential Pseudomonas aeruginosa isolates from chronically infected patients with cystic fibrosis were analyzed by thin-layer chromatography. It is demonstrated that both the amounts and the types of molecules synthesized by isolates from...

Controlled molecules for X-ray diffraction experiments at free-electron lasers

International Nuclear Information System (INIS)

Stern, Stephan

2013-12-01

X-ray diffractive imaging is at the very heart of materials science and has been utilized for decades to solve unknown molecular structures. Nowadays, it serves as the key method of structural biology to solve molecular structures of large biological molecules comprising several thousand or even millions of atoms. However, X-ray diffraction from isolated molecules is very weak. Therefore, the regular and periodic arrangement of a huge number of identical copies of a certain molecule of interest within a crystal lattice has been a necessary condition in order to exploit Bragg diffraction of X-rays. This results in a huge increase in scattered signal and a strongly improved signal-to-noise ratio compared to diffraction from non-crystalline samples. The major bottleneck of structural biology is that many of biologically interesting molecules refuse to form crystals of sufficient size to be used at synchrotron X-ray lightsources. However, novel X-ray free-electron lasers (XFELs), which became operational very recently, promise to address this issue. X-ray pulses provided by XFELs are many orders of magnitude more intense than X-ray pulses from a synchrotron source and at the same time as short as only several tens of femtoseconds. Combined with wavelengths in the nm-pm range, XFELs are well-suited to study ultrafast atomic and molecular dynamics. Additionally, the ultrashort pulses can be utilized to circumvent the damage threshold which set a limit to the incident intensity in X-ray diffraction experiments before. At XFELs, though eventually destroying the investigated sample, no significant sample deterioration happens on the ultrashort timescale of the XFEL pulse and the measured diffraction pattern is due to an (almost) unharmed sample. In the framework of this thesis, the approach of utilizing the highly intense XFEL pulses for X-ray diffraction of weakly-scattering non-crystalline samples was taken to the limit of small isolated molecules. X-ray diffraction was

Controlled molecules for X-ray diffraction experiments at free-electron lasers

Energy Technology Data Exchange (ETDEWEB)

Stern, Stephan

2013-12-15

X-ray diffractive imaging is at the very heart of materials science and has been utilized for decades to solve unknown molecular structures. Nowadays, it serves as the key method of structural biology to solve molecular structures of large biological molecules comprising several thousand or even millions of atoms. However, X-ray diffraction from isolated molecules is very weak. Therefore, the regular and periodic arrangement of a huge number of identical copies of a certain molecule of interest within a crystal lattice has been a necessary condition in order to exploit Bragg diffraction of X-rays. This results in a huge increase in scattered signal and a strongly improved signal-to-noise ratio compared to diffraction from non-crystalline samples. The major bottleneck of structural biology is that many of biologically interesting molecules refuse to form crystals of sufficient size to be used at synchrotron X-ray lightsources. However, novel X-ray free-electron lasers (XFELs), which became operational very recently, promise to address this issue. X-ray pulses provided by XFELs are many orders of magnitude more intense than X-ray pulses from a synchrotron source and at the same time as short as only several tens of femtoseconds. Combined with wavelengths in the nm-pm range, XFELs are well-suited to study ultrafast atomic and molecular dynamics. Additionally, the ultrashort pulses can be utilized to circumvent the damage threshold which set a limit to the incident intensity in X-ray diffraction experiments before. At XFELs, though eventually destroying the investigated sample, no significant sample deterioration happens on the ultrashort timescale of the XFEL pulse and the measured diffraction pattern is due to an (almost) unharmed sample. In the framework of this thesis, the approach of utilizing the highly intense XFEL pulses for X-ray diffraction of weakly-scattering non-crystalline samples was taken to the limit of small isolated molecules. X-ray diffraction was

Ion transmission in a linear radiofrequency spectrometer

International Nuclear Information System (INIS)

Gomet, J.-C.

1975-01-01

A linear radiofrequency spectrometer is used for the purpose of experimental determination of the absolute ionization cross sections of various ions obtained by electron impact on polyatomic molecules. The transmission of the apparatus is studied: it does not only depend on the mass resolution of the spectrometer, but also on the nature of ions. It is affected by charge transfers, especially for the parent ions. An empiric way of correction of the apparatus function is given which allows the use at 10 -6 Torr [fr

Spectroscopic characterization of matrix isolated transient species

Science.gov (United States)

Lue, Christopher J.

Part I describes the electronic spectra of various actinide containing compounds isolated in solid Ar using laser induced fluorescence (LIF) spectroscopy. The IR spectra for many of the same molecules were also recorded to aid in the identification of the fluorescing species in the LIF spectra. LIF spectra of UO2 isolated in solid Ar were recorded to investigate the interactions between actinide compounds and the rare gas matrix host. At the time of the experiments, it had been proposed that for UO2 and CUO, the interactions between the actinide containing molecule and Ar were strong enough to reorder the low-lying electronic states of the molecule. The experiments presented here showed no evidence of a reordering of low-lying electronic states based on comparison of the matrix spectra with theoretical predictions and gas phase spectra. An attempt to observe fluorescence from higher order uranium oxides was undertaken. A matrix was made by ablating U metal in a 1.0% O2/Ar mixture. UO3 was a probable molecule formed in the experiment. And, while absorptions belonging to UO3 were observed in IR spectra, LIF from the same matrix provided evidence that another molecule was fluorescing. Two different vibrational frequencies observed in the U-O symmetric stretching region were indicative of at least two low-lying electronic states in fluorescing molecule. UO3 is a closed shell molecule, and it is unlikely that it has any low-lying electronic states. Instead, the fluorescence was attributed to the open shell species (UO2)+(O2) -. LIF and IR spectra of thermally vaporized UCl4 isolated in solid Ar were recorded. UCl4 contains U(IV), which is the most stable oxidation state other than U(VI). Before these experiments, no fluorescence had been recorded that could be attributed to UCl4. Based on the observed vibrational frequencies in the fluorescence bands and the lifetime of the fluorescence, it was determine that there was at least two different fluorescing species. The

Electron-excited molecule interactions

International Nuclear Information System (INIS)

Christophorou, L.G.; Tennessee Univ., Knoxville, TN

1991-01-01

In this paper the limited but significant knowledge to date on electron scattering from vibrationally/rotationally excited molecules and electron scattering from and electron impact ionization of electronically excited molecules is briefly summarized and discussed. The profound effects of the internal energy content of a molecule on its electron attachment properties are highlighted focusing in particular on electron attachment to vibrationally/rotationally and to electronically excited molecules. The limited knowledge to date on electron-excited molecule interactions clearly shows that the cross sections for certain electron-molecule collision processes can be very different from those involving ground state molecules. For example, optically enhanced electron attachment studies have shown that electron attachment to electronically excited molecules can occur with cross sections 10 6 to 10 7 times larger compared to ground state molecules. The study of electron-excited molecule interactions offers many experimental and theoretical challenges and opportunities and is both of fundamental and technological significance. 54 refs., 15 figs

Antibiofilm and antibacterial effects of specific chitosan molecules on Staphylococcus aureus isolates associated with bovine mastitis

Science.gov (United States)

Asli, Abdelhamid; Brouillette, Eric; Ster, Céline; Ghinet, Mariana Gabriela; Brzezinski, Ryszard; Lacasse, Pierre; Jacques, Mario

2017-01-01

Staphylococcus aureus is one of the major pathogens causing bovine intramammary infections (IMIs) and mastitis. Mastitis is the primary cause for the use of antibiotics in dairy farms but therapeutic failure is often observed. One of the reasons for the lack of effectiveness of antibiotic therapy despite the observed susceptibility of bacterial isolates in vitro are bacterial biofilms. In this study, we used chitosan of well-defined molecular weight (0.4–0.6, 1.3, 2.6 and 4.0 kDa) and investigated their antibiofilm and antibacterial activities in in vitro and in vivo models related to S. aureus IMIs. A chitosan of at least 6 units of glucosamine was necessary for maximum antibacterial activity. The 2.6 and 4.0 kDa forms were able to prevent biofilm production by the biofilm hyperproducer strain S. aureus 2117 and a bovine MRSA (methicillin-resistant S. aureus). The intramammary administration of the 2.6 kDa chitosan showed no adverse effects in mice or in cows, as opposed to the slight inflammatory effect observed in mammary glands with the 4.0 kDa derivative. The 2.6 kDa chitosan killed bacteria embedded in pre-established biofilms in a dose-dependent manner with a >3 log10 reduction in CFU at 4 mg/ml. Also, the 2.6 kDa chitosan could prevent the persistence of the internalized MRSA into the mammary epithelial cell line MAC-T. An in vitro checkerboard assay showed that the 2.6 kDa chitosan produced a synergy with the macrolide class of antibiotics (e.g., tilmicosin) and reduced the MIC of both molecules by 2–8 times. Finally, the intramammary administration of the 2.6 kDa chitosan alone (P<0.01) or in combination with tilmicosin (P<0.0001) reduced the colonization of mammary glands in a murine IMI model. Our results suggest that the use of chitosan alone or in combination with a low dose of a macrolide could help reduce antibiotic use in dairy farms. PMID:28486482

Antibiofilm and antibacterial effects of specific chitosan molecules on Staphylococcus aureus isolates associated with bovine mastitis.

Directory of Open Access Journals (Sweden)

Abdelhamid Asli

Full Text Available Staphylococcus aureus is one of the major pathogens causing bovine intramammary infections (IMIs and mastitis. Mastitis is the primary cause for the use of antibiotics in dairy farms but therapeutic failure is often observed. One of the reasons for the lack of effectiveness of antibiotic therapy despite the observed susceptibility of bacterial isolates in vitro are bacterial biofilms. In this study, we used chitosan of well-defined molecular weight (0.4-0.6, 1.3, 2.6 and 4.0 kDa and investigated their antibiofilm and antibacterial activities in in vitro and in vivo models related to S. aureus IMIs. A chitosan of at least 6 units of glucosamine was necessary for maximum antibacterial activity. The 2.6 and 4.0 kDa forms were able to prevent biofilm production by the biofilm hyperproducer strain S. aureus 2117 and a bovine MRSA (methicillin-resistant S. aureus. The intramammary administration of the 2.6 kDa chitosan showed no adverse effects in mice or in cows, as opposed to the slight inflammatory effect observed in mammary glands with the 4.0 kDa derivative. The 2.6 kDa chitosan killed bacteria embedded in pre-established biofilms in a dose-dependent manner with a >3 log10 reduction in CFU at 4 mg/ml. Also, the 2.6 kDa chitosan could prevent the persistence of the internalized MRSA into the mammary epithelial cell line MAC-T. An in vitro checkerboard assay showed that the 2.6 kDa chitosan produced a synergy with the macrolide class of antibiotics (e.g., tilmicosin and reduced the MIC of both molecules by 2-8 times. Finally, the intramammary administration of the 2.6 kDa chitosan alone (P<0.01 or in combination with tilmicosin (P<0.0001 reduced the colonization of mammary glands in a murine IMI model. Our results suggest that the use of chitosan alone or in combination with a low dose of a macrolide could help reduce antibiotic use in dairy farms.

Phenotypic modulation of auto-reactive cells by insertion of tolerogenic molecules via MSC-derived exosomes.

Science.gov (United States)

Mokarizadeh, Aram; Delirezh, Nowruz; Morshedi, Ahhmad; Mosayebi, Ghasem; Farshid, Amir-Abbas; Dalir-Naghadeh, Bahram

2012-01-01

Auto-reactive cells-mediated immune responses are responsible for the current tissue damages during autoimmunity. Accordingly, functional modulation of auto-reactive cells has been a pivotal aim in many of recent studies. In the current study, we investigated the possibility for insertion of regulatory molecules onto auto-reactive cells through exosomal nano-shuttles as a novel approach for phenotype modification of auto-reactive cells. The exosomes were isolated from supernatant of mesenchymal stem cells culture. Resultant exosomes co-cultured with lymphocytes were harvested from established EAE mice in the presence of antigenic MOG35-55 peptide. After 24 hr, insertion of exosomal tolerogenic molecules (PD-L1, TGF-β, galectin-1) onto auto-reactive cells were explored through flow cytometry. The potency of exosomal inserted membrane molecules to modulate phenotype of auto-reactive lymphocytes was assessed upon ELISA test for their-derived cytokines IFN-γ and IL-17. Incorporation of exosomal molecules into lymohocytes' membrane was confirmed by flow cytometric analyses for surface levels of mentioned molecules. Additionally, the decreased secretion of IFN-γ and IL-17 were detected in exosome pre-treated lymphocytes upon stimulation with MOG peptide. Mesenchymal stem cells -derived exosomes showed to be efficient organelles for insertion of bioactive tolerogenic molecules onto auto-reactive cells and modulation of their phenotypes.

Along the Central Dogma-Controlling Gene Expression with Small Molecules.

Science.gov (United States)

Schneider-Poetsch, Tilman; Yoshida, Minoru

2018-05-04

The central dogma of molecular biology, that DNA is transcribed into RNA and RNA translated into protein, was coined in the early days of modern biology. Back in the 1950s and 1960s, bacterial genetics first opened the way toward understanding life as the genetically encoded interaction of macromolecules. As molecular biology progressed and our knowledge of gene control deepened, it became increasingly clear that expression relied on many more levels of regulation. In the process of dissecting mechanisms of gene expression, specific small-molecule inhibitors played an important role and became valuable tools of investigation. Small molecules offer significant advantages over genetic tools, as they allow inhibiting a process at any desired time point, whereas mutating or altering the gene of an important regulator would likely result in a dead organism. With the advent of modern sequencing technology, it has become possible to monitor global cellular effects of small-molecule treatment and thereby overcome the limitations of classical biochemistry, which usually looks at a biological system in isolation. This review focuses on several molecules, especially natural products, that have played an important role in dissecting gene expression and have opened up new fields of investigation as well as clinical venues for disease treatment. Expected final online publication date for the Annual Review of Biochemistry Volume 87 is June 20, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Single molecule tracking fluorescence microscopy in mitochondria reveals highly dynamic but confined movement of Tom40

Science.gov (United States)

Kuzmenko, Anton; Tankov, Stoyan; English, Brian P.; Tarassov, Ivan; Tenson, Tanel; Kamenski, Piotr; Elf, Johan; Hauryliuk, Vasili

2011-12-01

Tom40 is an integral protein of the mitochondrial outer membrane, which as the central component of the Translocase of the Outer Membrane (TOM) complex forms a channel for protein import. We characterize the diffusion properties of individual Tom40 molecules fused to the photoconvertable fluorescent protein Dendra2 with millisecond temporal resolution. By imaging individual Tom40 molecules in intact isolated yeast mitochondria using photoactivated localization microscopy with sub-diffraction limited spatial precision, we demonstrate that Tom40 movement in the outer mitochondrial membrane is highly dynamic but confined in nature, suggesting anchoring of the TOM complex as a whole.

GLUT2 in pancreatic islets: crucial target molecule in diabetes induced with multiple low doses of streptozotocin in mice.

Science.gov (United States)

Wang, Z; Gleichmann, H

1998-01-01

In mice, diabetes can be induced by multiple low doses of streptozotocin (MLD-STZ), i.e., 40 mg/kg body wt on each of 5 consecutive days. In this model, diabetes develops only when STZ induces both beta-cell toxicity and T-cell-dependent immune reactions. The target molecule(s) of MLD-STZ-induced beta-cell toxicity are not known, however. In this study, we report that GLUT2 is a target molecule for MLD-STZ toxicity. Ex vivo, a gradual decrement of both GLUT2 protein and mRNA expression was found in pancreatic islets isolated from MLD-STZ-treated C57BL/6 male mice, whereas mRNA expression of beta-actin, glucokinase, and proinsulin remained unaffected. Significant reduction of both GLUT2 protein and mRNA expression was first noted 1 day after the third STZ injection, clearly preceding the onset of hyperglycemia. The extent of reduction increased with the number of STZ injections administered and increased over time, after the last, i.e., fifth, STZ injection. The STZ-induced reduction of GLUT2 protein and mRNA was not due to an essential loss of beta-cells, because ex vivo, not only the total RNA yield and protein content in isolated islets, but also proinsulin mRNA expression, failed to differ significantly in the differently treated groups. Furthermore, islets isolated from MLD-STZ-treated donors responded to the nonglucose secretagogue arginine in a pattern similar to that of solvent-treated donors. Interestingly, the MLD-STZ-induced reduction of both GLUT2 protein and mRNA was prevented by preinjecting mice with 5-thio-D-glucose before each STZ injection. Apparently, GLUT2 is a crucial target molecule of MLD-STZ toxicity, and this toxicity seems to precede the immune reactions against beta-cells.

Ultra-cold molecule production

International Nuclear Information System (INIS)

Ramirez-Serrano, Jamie; Chandler, David W.; Strecker, Kevin; Rahn, Larry A.

2005-01-01

The production of Ultra-cold molecules is a goal of many laboratories through out the world. Here we are pursuing a unique technique that utilizes the kinematics of atomic and molecular collisions to achieve the goal of producing substantial numbers of sub Kelvin molecules confined in a trap. Here a trap is defined as an apparatus that spatially localizes, in a known location in the laboratory, a sample of molecules whose temperature is below one degree absolute Kelvin. Further, the storage time for the molecules must be sufficient to measure and possibly further cool the molecules. We utilize a technique unique to Sandia to form cold molecules from near mass degenerate collisions between atoms and molecules. This report describes the progress we have made using this novel technique and the further progress towards trapping molecules we have cooled

Emerging greener extraction systems for fungal pigments isolation

OpenAIRE

Lebeau , Juliana; Venkatachalam , Mekala; Fouillaud , Mireille; Dufossé , Laurent; Caro , Yanis

2016-01-01

International audience; Filamentous fungi produce a mixture of various metabolites such as pigments, fatty acids, proteins and other cellular metabolites. Thus, extraction and isolation of the pigmented molecules of interest are necessary steps before proceeding to any further utilization of these metabolites for commercial applications. Pigments can be stored within the biomass, excreted in the fermentation broth or both, suggesting that extraction methods need to be developed accordingly to...

Molecules in stars

International Nuclear Information System (INIS)

Tsuji, T.

1986-01-01

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

Water and nonelectrolyte permeability of isolated rat hepatocytes

International Nuclear Information System (INIS)

Alpini, G.; Garrick, R.A.; Jones, M.J.; Nunes, R.; Tavoloni, N.

1986-01-01

We have measured the diffusive permeability coefficients of isolated rat hepatocytes to 3 H 2 O, [ 14 C]urea, [ 14 C]erythritol, [ 14 C]mannitol, [ 3 H]sucrose, and [ 3 H]inulin, employing a technique previously developed for erythrocytes (Redwood et al., J. Gen. Physiol 64:706-729, 1974). Diffusion coefficients for the tracer molecules were measured in packed hepatocytes, supernatant fluid, and intracellular medium (lysed hepatocytes) and were calculated assuming one-dimensional semi-infinite diffusion through a homogeneous medium. By applying the series-parallel pathway model, the following permeability coefficients (10(-5) cm/sec) for the hepatocyte plasma membrane were obtained. 3 H 2 O, 98.6 +/- 18.4; [ 14 C]urea, 18.2 +/- 5.3; [ 14 C]erythritol, 4.8 +/- 1.6; [ 14 C]mannitol, 3.1 +/- 1.4; [ 3 H]sucrose, 0; [ 3 H]inulin, 0. These results indicate that isolated rat hepatocytes are highly permeable to water and polar nonelectrolytes, when compared with other transporting epithelia. This relatively high cellular permeability is consistent with a model in which nonelectrolyte permeation is via an aqueous pathway of equivalent pore diameter of 8-12 A. The finding that [ 14 C]erythritol and [ 14 C]mannitol cross the hepatocyte plasma membrane indicates that these molecules enter the bile canaliculus through the transcellular route. Conversely, the failure of [ 3 H]sucrose and [ 3 H]inulin to permeate the hepatocyte in the isolated condition supports the concept that biliary entry of these large carbohydrates, at least that fraction which cannot be accounted for by a vesicular mechanism, must occur via the transjunctional shunt pathway

An anti-CCR5 monoclonal antibody and small molecule CCR5 antagonists synergize by inhibiting different stages of human immunodeficiency virus type 1 entry

International Nuclear Information System (INIS)

Safarian, Diana; Carnec, Xavier; Tsamis, Fotini; Kajumo, Francis; Dragic, Tatjana

2006-01-01

HIV-1 coreceptors are attractive targets for novel antivirals. Here, inhibition of entry by two classes of CCR5 antagonists was investigated. We confirmed previous findings that HIV-1 isolates vary greatly in their sensitivity to small molecule inhibitors of CCR5-mediated entry, SCH-C and TAK-779. In contrast, an anti-CCR5 monoclonal antibody (PA14) similarly inhibited entry of diverse viral isolates. Sensitivity to small molecules was V3 loop-dependent and inversely proportional to the level of gp120 binding to CCR5. Moreover, combinations of the MAb and small molecules were highly synergistic in blocking HIV-1 entry, suggesting different mechanisms of action. This was confirmed by time course of inhibition experiments wherein the PA14 MAb and small molecules were shown to inhibit temporally distinct stages of CCR5 usage. We propose that small molecules inhibit V3 binding to the second extracellular loop of CCR5, whereas PA14 preferentially inhibits subsequent events such as CCR5 recruitment into the fusion complex or conformational changes in the gp120-CCR5 complex that trigger fusion. Importantly, our findings suggest that combinations of CCR5 inhibitors with different mechanisms of action will be central to controlling HIV-1 infection and slowing the emergence of resistant strains

Accurate Calculations of Rotationally Inelastic Scattering Cross Sections Using Mixed Quantum/Classical Theory.

Science.gov (United States)

Semenov, Alexander; Babikov, Dmitri

2014-01-16

For computational treatment of rotationally inelastic scattering of molecules, we propose to use the mixed quantum/classical theory, MQCT. The old idea of treating translational motion classically, while quantum mechanics is used for rotational degrees of freedom, is developed to the new level and is applied to Na + N2 collisions in a broad range of energies. Comparison with full-quantum calculations shows that MQCT accurately reproduces all, even minor, features of energy dependence of cross sections, except scattering resonances at very low energies. The remarkable success of MQCT opens up wide opportunities for computational predictions of inelastic scattering cross sections at higher temperatures and/or for polyatomic molecules and heavier quenchers, which is computationally close to impossible within the full-quantum framework.

Molecule Matters

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 14; Issue 4. Molecule Matters – van der Waals Molecules - History and Some Perspectives on Intermolecular Forces. E Arunan. Feature Article Volume 14 Issue 4 April 2009 pp 346-356 ...

Spins of adsorbed molecules investigated by the detection of Kondo resonance

Science.gov (United States)

Komeda, Tadahiro

2014-12-01

Surface magnetism has been one of the platforms to explore the magnetism in low dimensions. It is also a key component for the development of quantum information processes, which utilizes the spin degree of freedom. The Kondo resonance is a phenomenon that is caused by an interaction between an isolated spin and conduction electrons. First observed in the 1930s as an anomalous increase in the low-temperature resistance of metals embedded with magnetic atoms, the Kondo physics mainly studied the effects of bulk magnetic impurities in the resistivity. In the last 15 years it has undergone a revival by a scanning tunneling microscope (STM) which enables the measurement of the Kondo resonance at surfaces using an atomic scale point contact. The detection of the Kondo resonance can be a powerful tool to explore surface magnetism. In this article, I review recent studies of the surface spin of adsorbed molecules by the detection of the Kondo resonance. Researches on metal phthalocyanine (MPc) and porphyrin molecules will be examined. In addition, the Kondo resonance for double-decker lanthanoide Pc molecules will be discussed. Some of the double-decker Pc molecules show single-molecule magnet (SMM) behavior, which attracts attention as a material for electronic devices. For both classes, the ligand plays a crucial role in determining the parameters of the Kondo resonance, such as the Kondo temperature and the change of the shape from peak to Fano-dip. In addition, the spin in delocalized molecular orbital forms the Kondo resonance, which shows significant differences from the Kondo resonance formed by the metal spins. Since molecular orbital can be tuned in a flexible manner by the design of the molecule, the Kondo resonance formed by delocalized molecular orbital might expand the knowledge of this field.

Density functional theory studies on the nano-scaled composites consisted of graphene and acyl hydrazone molecules

Science.gov (United States)

Ren, J. L.; Zhou, L.; Lv, Z. C.; Ding, C. H.; Wu, Y. H.; Bai, H. C.

2016-07-01

Graphene, which is the first obtained single atomic layer 2D materials, has drawn a great of concern in nano biotechnology due to the unique property. On one hand, acyl hydrazone compounds belonging to the Schif bases have aroused considerable attention in medicine, pharmacy, and analytical reagent. However, few understanding about the interaction between graphene and acyl hydrazone molecules is now available. And such investigations are much crucial for the applications of these new nano-scaled composites. The current work revealed theoretical investigations on the nano-scaled composites built by acyl hydrazone molecules loaded on the surface of graphene. The relative energy, electronic property and the interaction between the counterparts of graphene/acyl hydrazone composites are investigated based on the density functional theory calculations. According to the obtained adsorption energy, the formation of the nano-scaled composite from the isolated graphene and acyl hydrazone molecule is exothermic, and thus it is energetically favorable to form these nano composites in viewpoint of total energy change. The frontier molecular orbital for the nano composite is mainly distributed at the graphene part, leading to that the energy levels of the frontier molecular orbital of the nano composites are very close to that of isolated graphene. Moreover, the counterpart interaction for the graphene/acyl hydrazone composites is also explored based on the discussions of orbital hybridization, charge redistribution and Van der Waals interaction.

Design of polymetallic uranium assemblies for the development of single molecule magnets

International Nuclear Information System (INIS)

Chatelain, Lucile

2016-01-01

The study of actinide chemistry is not only essential for the development of nuclear fuel, nuclear fuel reprocessing or environmental clean up, but also for the understanding of fundamental actinide/ligand interactions and multiple bounding. The magnetic properties of polynuclear actinide molecules are of significant interest to investigate the magnetic communication between the metallic centres. Furthermore, they are highly promising for the design of molecular magnets. Uranium undergoes redox reactions due to a wide range of available oxidation states and easily forms polynuclear assemblies. However, only a few controlled synthetic routes towards these polynuclear uranium assemblies are described in the literature. In this context, the first part of this work was dedicated to the synthesis of oxo/hydroxo uranium clusters from the controlled hydrolysis of tetravalent uranium in the presence of an environmentally relevant ligand. This led to the synthesis of clusters with novel topologies, for which size could be varied as a function of the reaction conditions employed. However, the obtained clusters do not behave as SMM. In order to gain a stronger interaction between metallic centres, the cation-cation interaction was used to rationally design polynuclear uranyl(V) complexes. The isolation of uranyl(V) complexes had been limited in the past by its disproportionation, however, a fine tuning of the organic ligand and reaction conditions finally allowed to stabilise uranyl(V). We used stable uranyl(V) units as building block to form heteronuclear complexes with 3d and 4f metals with polymeric or discrete structures. The study of the magnetic properties of the uranium polynuclear assemblies was carried out and revealed single molecule or chain magnet behaviours with high energy barriers. The uranyl(V) unit was also used as a structural model for the more radioactive neptunium element, allowing the isolation of an isostructural trinuclear neptunyl(V) assembly in

Effects of lysosomal inhibitors on 125I-insulin and 125I-asialofetuin degradation by the isolated, perfused rat liver and isolated rat hepatocytes

International Nuclear Information System (INIS)

Ward, W.F.; Moss, A.L.

1985-01-01

To further evaluate the role of the lysosomal system in insulin degradation, the authors have compared the effects of inhibitors of lysosomal function on the degradation of 125 I-insulin with 125 I-asialofetuin, a lysosomally targeted molecule, by the intact, perfused rat liver and the isolated rat hepatocyte. The inhibitors employed were chloroquine ( 125 microM), NH 4 Cl (10 mM), and leupeptin (50 micrograms/ml). In the intact, perfused liver the observed inhibition of 125 I-asialofetuin degradation at 30 min was as follows: chloroquine, 38%; NH 4 Cl, 32%; and leupeptin, 86%. Chloroquine also inhibited 125 I-insulin degradation in the intact, perfused liver (29%), but NH 4 Cl and leupeptin had no effect. Using the isolated hepatocyte, the observed values for inhibition of 125I-asialofetuin at 60 min were: chloroquine, 85%; NH 4 Cl, 76%; and leupeptin, 81%. Chloroquine produced a 28% inhibition of 125I-insulin degradation, while NH 4 Cl and leupeptin had no effect. Chloroquine and NH 4 Cl decreased cell-associated radioactivity when isolated hepatocytes were incubated with 125I-asialofetuin (leupeptin had no effect), whereas chloroquine caused a 107% increase in cell-associated radioactivity when 125I-insulin was added to the incubation media (NH 4 Cl and leupeptin had no effect). These results indicate that the effects of chloroquine on insulin degradation are an extralysosomal action and that lysosomes appear not to be involved in the physiologic degradation of the insulin molecule

Formation of Ultracold Molecules

Energy Technology Data Exchange (ETDEWEB)

Cote, Robin [Univ. of Connecticut, Storrs, CT (United States)

2016-01-28

Advances in our ability to slow down and cool atoms and molecules to ultracold temperatures have paved the way to a revolution in basic research on molecules. Ultracold molecules are sensitive of very weak interactions, even when separated by large distances, which allow studies of the effect of those interactions on the behavior of molecules. In this program, we have explored ways to form ultracold molecules starting from pairs of atoms that have already reached the ultracold regime. We devised methods that enhance the efficiency of ultracold molecule production, for example by tuning external magnetic fields and using appropriate laser excitations. We also investigates the properties of those ultracold molecules, especially their de-excitation into stable molecules. We studied the possibility of creating new classes of ultra-long range molecules, named macrodimers, thousand times more extended than regular molecules. Again, such objects are possible because ultra low temperatures prevent their breakup by collision. Finally, we carried out calculations on how chemical reactions are affected and modified at ultracold temperatures. Normally, reactions become less effective as the temperature decreases, but at ultracold temperatures, they can become very effective. We studied this counter-intuitive behavior for benchmark chemical reactions involving molecular hydrogen.

Enhancement of strong-field multiple ionization in the vicinity of the conical intersection in 1,3-cyclohexadiene ring opening

International Nuclear Information System (INIS)

Petrovic, Vladimir S.; Kim, Jaehee; Schorb, Sebastian; White, James; Cryan, James P.; Zipp, Lucas; Glownia, J. Michael; Broege, Douglas; Miyabe, Shungo; Tao, Hongli; Martinez, Todd; Bucksbaum, Philip H.

2013-01-01

Nonradiative energy dissipation in electronically excited polyatomic molecules proceeds through conical intersections, loci of degeneracy between electronic states. We observe a marked enhancement of laser-induced double ionization in the vicinity of a conical intersection during a non-radiative transition. We measured double ionization by detecting the kinetic energy of ions released by laser-induced strong-field fragmentation during the ring-opening transition between 1,3-cyclohexadiene and 1,3,5-hexatriene. The enhancement of the double ionization correlates with the conical intersection between the HOMO and LUMO orbitals

Applied group theory selected readings in physics

CERN Document Server

Cracknell, Arthur P

1968-01-01

Selected Readings in Physics: Applied Group Theory provides information pertinent to the fundamental aspects of applied group theory. This book discusses the properties of symmetry of a system in quantum mechanics.Organized into two parts encompassing nine chapters, this book begins with an overview of the problem of elastic vibrations of a symmetric structure. This text then examines the numbers, degeneracies, and symmetries of the normal modes of vibration. Other chapters consider the conditions under which a polyatomic molecule can have a stable equilibrium configuration when its electronic

Some aspects of vacuum ultraviolet radiation physics

CERN Document Server

Damany, Nicole; Vodar, Boris

2013-01-01

Some Aspects of Vacuum Ultraviolet Radiation Physics presents some data on the state of research in vacuum ultraviolet radiation in association with areas of physics. Organized into four parts, this book begins by elucidating the optical properties of solids in the vacuum ultraviolet region (v.u.v.), particularly the specific methods of determination of optical constants in v.u.v., the properties of metals, and those of ionic insulators. Part II deals with molecular spectroscopy, with emphasis on the spectra of diatomic and simple polyatomic molecules, paraffins, and condensed phases. Part III

The Role of Molecules in Low Temperature Plasmas for Lighting

International Nuclear Information System (INIS)

Lapatovich, Walter P.

2007-01-01

High intensity discharge (HID) lamps are low temperature (∼0.5eV), weakly ionized plasmas sustained in a refractory but light transmissive envelope for the purpose of converting electrical power into visible radiation. For commercial applications this conversion must occur with good efficiency and with sufficient spectral content throughout the visible (380-780nm) to permit the light so generated to render colors in a fashion comparable to natural sunlight. These goals are often achieved by adding multiple metals to a basic mercury discharge. Because the vapor pressure of most metals is very much lower than mercury itself, chemical compounds containing the desired metals, and having higher vapor pressures are used to introduce the material into the basic discharge. Complexing agents which further improve the vapor pressure are used to enhance the amount of metals in the discharge. The metal compound and complexes are usually polyatomic species which vaporize and subsequently dissociate as they diffuse into the bulk plasma. Under the approximation of local thermodynamic equilibrium (LTE) the particles are in equilibrium, but not with the radiation Held. Strong thermal (106K/m) and density gradients are sustained in the discharge. Atomic and molecular radiation produced in the high temperature core transits through colder gas regions before exiting the lamp. In these regions where the complex molecular species exists in an undissociated state, bound-free transitions can result in energy being effectively converted from light radiation into heat in the mantle. Bound-bound transitions In Identifiable molecules can result in modification of the spectral output in unpredictable and counter-intuitive ways. Examples of completing agents and their effect on the spectral output of typical rare-earth containing HID lamps will be given. The melt composition and the complexing agents themselves may change with time, as chemical reactions in the lamp occur, and their benefit

Atom and Bond Fukui Functions and Matrices: A Hirshfeld-I Atoms-in-Molecule Approach.

Science.gov (United States)

Oña, Ofelia B; De Clercq, Olivier; Alcoba, Diego R; Torre, Alicia; Lain, Luis; Van Neck, Dimitri; Bultinck, Patrick

2016-09-19

The Fukui function is often used in its atom-condensed form by isolating it from the molecular Fukui function using a chosen weight function for the atom in the molecule. Recently, Fukui functions and matrices for both atoms and bonds separately were introduced for semiempirical and ab initio levels of theory using Hückel and Mulliken atoms-in-molecule models. In this work, a double partitioning method of the Fukui matrix is proposed within the Hirshfeld-I atoms-in-molecule framework. Diagonalizing the resulting atomic and bond matrices gives eigenvalues and eigenvectors (Fukui orbitals) describing the reactivity of atoms and bonds. The Fukui function is the diagonal element of the Fukui matrix and may be resolved in atom and bond contributions. The extra information contained in the atom and bond resolution of the Fukui matrices and functions is highlighted. The effect of the choice of weight function arising from the Hirshfeld-I approach to obtain atom- and bond-condensed Fukui functions is studied. A comparison of the results with those generated by using the Mulliken atoms-in-molecule approach shows low correlation between the two partitioning schemes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Exotic helium molecules; Molecules exotiques d'helium

Energy Technology Data Exchange (ETDEWEB)

Portier, M

2007-12-15

We study the photo-association of an ultracold cloud of magnetically trapped helium atoms: pairs of colliding atoms interact with one or two laser fields to produce a purely long range {sup 4}He{sub 2}(2{sup 3}S{sub 1}-2{sup 3}P{sub 0}) molecule, or a {sup 4}He{sub 2}(2{sup 3}S{sub 1}-2{sup 3}S{sub 1}) long range molecule. Light shifts in one photon photo-association spectra are measured and studied as a function of the laser polarization and intensity, and the vibrational state of the excited molecule. They result from the light-induced coupling between the excited molecule, and bound and scattering states of the interaction between two metastable atoms. Their analysis leads to the determination of the scattering length a = (7.2 {+-} 0.6) ruling collisions between spin polarized atoms. The two photon photo-association spectra show evidence of the production of polarized, long-range {sup 4}He{sub 2}(2{sup 3}S{sub 1}-2{sup 3}S{sub 1}) molecules. They are said to be exotic as they are made of two metastable atoms, each one carrying a enough energy to ionize the other. The corresponding lineshapes are calculated and decomposed in sums and products of Breit-Wigner and Fano profiles associated to one and two photon processes. The experimental spectra are fit, and an intrinsic lifetime {tau} = (1.4 {+-} 0.3) {mu}s is deduced. It is checked whether this lifetime could be limited by spin-dipole induced Penning autoionization. This interpretation requires that there is a quasi-bound state close to the dissociation threshold in the singlet interaction potential between metastable helium atoms for the theory to match the experiment. (author)

Resistance of a human immunodeficiency virus type 1 isolate to a small molecule CCR5 inhibitor can involve sequence changes in both gp120 and gp41

International Nuclear Information System (INIS)

Anastassopoulou, Cleo G.; Ketas, Thomas J.; Depetris, Rafael S.; Thomas, Antonia M.; Klasse, Per Johan; Moore, John P.

2011-01-01

Here, we describe the genetic pathways taken by a human immunodeficiency virus type 1 (HIV-1) isolate, D101.12, to become resistant to the small molecule CCR5 inhibitor, vicriviroc (VCV), in vitro. Resistant D101.12 variants contained at least one substitution in the gp120 V3 region (H308P), plus one of two patterns of gp41 sequence changes involving the fusion peptide (FP) and a downstream residue: G514V+V535M or M518V+F519L+V535M. Studies of Env-chimeric and point-substituted viruses in peripheral blood mononuclear cells (PBMC) and TZM-bl cells showed that resistance can arise from the cooperative action of gp120 and gp41 changes, while retaining CCR5 usage. Modeling the VCV inhibition data from the two cell types suggests that D101.12 discriminates between high- and low-VCV affinity forms of CCR5 less than D1/85.16, a resistant virus with three FP substitutions.

The status of molecules

International Nuclear Information System (INIS)

Barnes, T.; Oak Ridge National Lab., TN; Tennessee Univ., Knoxville, TN

1994-06-01

This report summarizes the experimental and theoretical status of hadronic molecules, which are weakly-bound states of two or more hadrons. We begin with a brief history of the subject and discuss a few good candidates, and then abstract some signatures for molecules which may be of interest in the classification of possible molecule states. Next we argue that a more general understanding of 2 → 2 hadron-hadron scattering amplitudes will be crucial for molecule searches, and discuss some of our recent work in this area. We conclude with a discussion of a few more recent molecule candidates (notably the f o (1710)) which are not well established as molecules but satisfy some of the expected signatures. (Author)

Strategy to discover diverse optimal molecules in the small molecule universe.

Science.gov (United States)

Rupakheti, Chetan; Virshup, Aaron; Yang, Weitao; Beratan, David N

2015-03-23

The small molecule universe (SMU) is defined as a set of over 10(60) synthetically feasible organic molecules with molecular weight less than ∼500 Da. Exhaustive enumerations and evaluation of all SMU molecules for the purpose of discovering favorable structures is impossible. We take a stochastic approach and extend the ACSESS framework ( Virshup et al. J. Am. Chem. Soc. 2013 , 135 , 7296 - 7303 ) to develop diversity oriented molecular libraries that can generate a set of compounds that is representative of the small molecule universe and that also biases the library toward favorable physical property values. We show that the approach is efficient compared to exhaustive enumeration and to existing evolutionary algorithms for generating such libraries by testing in the NKp fitness landscape model and in the fully enumerated GDB-9 chemical universe containing 3 × 10(5) molecules.

Isolation and Characterization of Serum Extracellular Vesicles (EVs from Atlantic Salmon Infected with Piscirickettsia Salmonis

Directory of Open Access Journals (Sweden)

Leidy Lagos

2017-12-01

Full Text Available Secretion of extracellular vesicles (EVs is a common feature of both eukaryotic and prokaryotic cells. Isolated EVs have been shown to contain different types of molecules, including proteins and nucleic acids, and are reported to be key players in intercellular communication. Little is known, however, of EV secretion in fish, or the effect of infection on EV release and content. In the present study, EVs were isolated from the serum of healthy and Piscirickettsia salmonis infected Atlantic salmon in order to evaluate the effect of infection on EV secretion. P. salmonis is facultative intracellular bacterium that causes a systemic infection disease in farmed salmonids. EVs isolated from both infected and non-infected fish had an average diameter of 230–300 nm, as confirmed by transmission electron microscopy, nanoparticle tracking, and flow cytometry. Mass spectrometry identified 180 proteins in serum EVs from both groups of fish. Interestingly, 35 unique proteins were identified in serum EVs isolated from the fish infected with P. salmonis. These unique proteins included proteasomes subunits, granulins, and major histocompatibility class I and II. Our results suggest that EV release could be part of a mechanism in which host stimulatory molecules are released from infected cells to promote an immune response.

Isolation of high quality graphene from Ru by solution phase intercalation

Science.gov (United States)

Koren, E.; Sutter, E.; Bliznakov, S.; Ivars-Barcelo, F.; Sutter, P.

2013-09-01

We introduce a method for isolating graphene grown on epitaxial Ru(0001)/α-Al2O3. The strong graphene/Ru(0001) coupling is weakened by electrochemically driven intercalation of hydrogen underpotentially deposited in aqueous KOH solution, which allows the penetration of water molecules at the graphene/Ru(0001) interface. Following these electrochemically driven processes, the graphene can be isolated by electrochemical hydrogen evolution and transferred to arbitrary supports. Raman and transport measurements demonstrate the high quality of the transferred graphene. Our results show that intercalation, typically carried out in vacuum, can be extended to solution environments for graphene processing under ambient conditions.

Proglobulin processing enzyme in vacuoles isolated from developing pumpkin cotyledons

International Nuclear Information System (INIS)

Hara-Nishimura, I.; Nishimura, M.

1987-01-01

The enzymic conversion of proglobulin to globulin catalyzed by the extracts of vacuoles isolated from developing pumpkin (Cucurbita sp. cv Kurokawa Amakuri Nankin) cotyledons was investigated. The endoplasmic reticulum fraction isolated from the developing cotyledons pulse-labeled with [ 35 S]methionine was shown to contain mainly the radiolabeled proglobulin, which was used as a substrate for assaying the proteolytic processing in vitro. The vacuolar extracts catalyzed the proteolytic processing of the proglobulin molecule to produce globulin containing two kinds of polypeptide chains, γ and δ. The pH optimum for the vacuole-mediated conversion was at pH 5.0. The proteolytic processing of proglobulin by the vacuolar extracts was inhibited in the presence of various thiol reagents, e.g. p-chloromercuribenzoate, N-ethylmaleimide, iodoacetic acid, Hg 2+ , and Cu 2+ , but not phenylmethylsulfonyl fluoride, EDTA, o-phenanthroline, leupeptin, antipain, pepstatin, chymostatin, or pumpkin trypsin inhibitor, and was activated in the presence of dithiothreitol and cysteine, indicating that the processing enzyme is a thiol protease. The suborganellar fractionation of the vacuoles showed that the processing activity was localized in the matrix fraction, but not in the membrane or crystalloid fractions. During the seed development, the enzyme was shown to increase, exhibiting the maximal activity at the late developmental stage. The matrix fraction of the protein bodies isolated from the dry castor bean (Ricinus communis) exhibited the processing activity toward the pumpkin proglobulin molecules in the same manner as that by the matrix fraction of pumpkin vacuoles

Small molecule screening platform for assessment of cardiovascular toxicity on adult zebrafish heart

Directory of Open Access Journals (Sweden)

Kitambi Satish

2012-03-01

Full Text Available Abstract Background Cardiovascular toxicity is a major limiting factor in drug development and requires multiple cost-effective models to perform toxicological evaluation. Zebrafish is an excellent model for many developmental, toxicological and regenerative studies. Using approaches like morpholino knockdown and electrocardiogram, researchers have demonstrated physiological and functional similarities between zebrafish heart and human heart. The close resemblance of the genetic cascade governing heart development in zebrafish to that of humans has propelled the zebrafish system as a cost-effective model to conduct various genetic and pharmacological screens on developing embryos and larvae. The current report describes a methodology for rapid isolation of adult zebrafish heart, maintenance ex vivo, and a setup to perform quick small molecule throughput screening, including an in-house implemented analysis script. Results Adult zebrafish were anesthetized and after rapid decapitation the hearts were isolated. The short time required for isolation of hearts allows dissection of multiple fishes, thereby obtaining a large sample size. The simple protocol for ex vivo culture allowed maintaining the beating heart for several days. The in-house developed script and spectral analyses allowed the readouts to be presented either in time domain or in frequency domain. Taken together, the current report offers an efficient platform for performing cardiac drug testing and pharmacological screens. Conclusion The new methodology presents a fast, cost-effective, sensitive and reliable method for performing small molecule screening. The variety of readouts that can be obtained along with the in-house developed analyses script offers a powerful setup for performing cardiac toxicity evaluation by researchers from both academics and industry.

Imaging a multidimensional multichannel potential energy surface: Photodetachment of H{sup −}(NH{sub 3}) and NH{sub 4}{sup −}

Energy Technology Data Exchange (ETDEWEB)

Hu, Qichi; Johnson, Christopher J.; Continetti, Robert E., E-mail: hguo@umn.edu, E-mail: rcontinetti@ucsd.edu [Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340 (United States); Song, Hongwei; Guo, Hua, E-mail: hguo@umn.edu, E-mail: rcontinetti@ucsd.edu [Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131 (United States); Li, Jun [School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044 (China)

2016-06-28

Probes of the Born-Oppenheimer potential energy surfaces governing polyatomic molecules often rely on spectroscopy for the bound regions or collision experiments in the continuum. A combined spectroscopic and half-collision approach to image nuclear dynamics in a multidimensional and multichannel system is reported here. The Rydberg radical NH{sub 4} and the double Rydberg anion NH{sub 4}{sup −} represent a polyatomic system for benchmarking electronic structure and nine-dimensional quantum dynamics calculations. Photodetachment of the H{sup −}(NH{sub 3}) ion-dipole complex and the NH{sub 4}{sup −} DRA probes different regions on the neutral NH{sub 4} PES. Photoelectron energy and angular distributions at photon energies of 1.17, 1.60, and 2.33 eV compare well with quantum dynamics. Photoelectron-photofragment coincidence experiments indicate dissociation of the nascent NH{sub 4} Rydberg radical occurs to H + NH{sub 3} with a peak kinetic energy of 0.13 eV, showing the ground state of NH{sub 4} to be unstable, decaying by tunneling-induced dissociation on a time scale beyond the present scope of multidimensional quantum dynamics.

Towards a Quantum Dynamical Study of the H_2O+H_2O Inelastic Collision: Representation of the Potential and Preliminary Results

Science.gov (United States)

Ndengue, Steve Alexandre; Dawes, Richard

2017-06-01

Water, an essential ingredient of life, is prevalent in space and various media. H_2O in the gas phase is the major polyatomic species in the interstellar medium (ISM) and a primary target of current studies of collisional dynamics. In recent years a number of theoretical and experimental studies have been devoted to H_2O-X (with X=He, H_2, D_2, Ar, ?) elastic and inelastic collisions in an effort to understand rotational distributions of H_2O in molecular clouds. Although those studies treated several abundant species, no quantum mechanical calculation has been reported to date for a nonlinear polyatomic collider. We present in this talk the preliminary steps toward this goal, using the H_2O molecule itself as our collider, the very accurate MB-Pol surface to describe the intermolecular interaction and the MultiConfiguration Time Dependent (MCTDH) algorithm to study the dynamics. One main challenge in this effort is the need to express the Potential Energy Surface (PES) in a sum-of-products form optimal for MCTDH calculations. We will describe how this was done and present preliminary results of state-to-state probabilities.

Vibronic coupling in ionized organic molecules: structural distortions and chemical reactions

International Nuclear Information System (INIS)

Williams, Ffrancon

2003-01-01

Ionized organic molecules (radical cations) in radiation chemistry are liable to undergo vibronic coupling whenever there is a relatively small energy gap (∼0.5-1.5 eV) between their ground and excited states. As a result of this mixing, the force constant for the symmetry-allowed vibrational mode that couples these states is lowered in the ground state of the radical cation so that deformation can take place more easily along this specific mode. This pseudo-Jahn-Teller effect can then result in a permanent structural distortion of the radical cation relative to the symmetry of the parent neutral molecule. It can also bring about an energetically favored pathway for a facile chemical rearrangement along a reaction coordinate defined by the coupling mode. Examples taken from matrix-isolation studies are used to illustrate these dramatic consequences of vibronic coupling in radical cations. Thus, the bicyclo[2.2.2]oct-2-ene and tetramethylurea radical cations are found to have twisted structures departing from the C 2v symmetry of their parent molecules, while the oxirane and bicyclo[1.1.1]pentane radical cations undergo ring-opening rearrangements along reaction coordinates that correspond to the deformational modes predicted by the pseudo-Jahn-Teller effect

Quorum sensing signaling molecules produced by reference and emerging soft-rot bacteria (Dickeya and Pectobacterium spp..

Directory of Open Access Journals (Sweden)

Alexandre Crépin

Full Text Available Several small diffusible molecules are involved in bacterial quorum sensing and virulence. The production of autoinducers-1 and -2, quinolone, indole and γ-amino butyrate signaling molecules was investigated in a set of soft-rot bacteria belonging to six Dickeya or Pectobacterium species including recent or emerging potato isolates.Using bacterial biosensors, immunoassay, and chromatographic analysis, we showed that soft-rot bacteria have the common ability to produce transiently during their exponential phase of growth the N-3-oxo-hexanoyl- or the N-3-oxo-octanoyl-l-homoserine lactones and a molecule of the autoinducer-2 family. Dickeya spp. produced in addition the indole-3-acetic acid in tryptophan-rich conditions. All these signaling molecules have been identified for the first time in the novel Dickeya solani species. In contrast, quinolone and γ-amino butyrate signals were not identified and the corresponding synthases are not present in the available genomes of soft-rot bacteria. To determine if the variations of signal production according to growth phase could result from expression modifications of the corresponding synthase gene, the respective mRNA levels were estimated by reverse transcriptase-PCR. While the N-acyl-homoserine lactone production is systematically correlated to the synthase expression, that of the autoinducer-2 follows the expression of an enzyme upstream in the activated methyl cycle and providing its precursor, rather than the expression of its own synthase.Despite sharing the S-adenosylmethionine precursor, no strong link was detected between the production kinetics or metabolic pathways of autoinducers-1 and -2. In contrast, the signaling pathway of autoinducer-2 seems to be switched off by the indole-3-acetic acid pathway under tryptophan control. It therefore appears that the two genera of soft-rot bacteria have similarities but also differences in the mechanisms of communication via the diffusible molecules

Quorum Sensing Signaling Molecules Produced by Reference and Emerging Soft-Rot Bacteria (Dickeya and Pectobacterium spp.)

Science.gov (United States)

Crépin, Alexandre; Barbey, Corinne; Beury-Cirou, Amélie; Hélias, Valérie; Taupin, Laure; Reverchon, Sylvie; Nasser, William; Faure, Denis; Dufour, Alain; Orange, Nicole; Feuilloley, Marc; Heurlier, Karin; Burini, Jean-François; Latour, Xavier

2012-01-01

Background Several small diffusible molecules are involved in bacterial quorum sensing and virulence. The production of autoinducers-1 and -2, quinolone, indole and γ-amino butyrate signaling molecules was investigated in a set of soft-rot bacteria belonging to six Dickeya or Pectobacterium species including recent or emerging potato isolates. Methodology/Principal Findings Using bacterial biosensors, immunoassay, and chromatographic analysis, we showed that soft-rot bacteria have the common ability to produce transiently during their exponential phase of growth the N-3-oxo-hexanoyl- or the N-3-oxo-octanoyl-l-homoserine lactones and a molecule of the autoinducer-2 family. Dickeya spp. produced in addition the indole-3-acetic acid in tryptophan-rich conditions. All these signaling molecules have been identified for the first time in the novel Dickeya solani species. In contrast, quinolone and γ-amino butyrate signals were not identified and the corresponding synthases are not present in the available genomes of soft-rot bacteria. To determine if the variations of signal production according to growth phase could result from expression modifications of the corresponding synthase gene, the respective mRNA levels were estimated by reverse transcriptase-PCR. While the N-acyl-homoserine lactone production is systematically correlated to the synthase expression, that of the autoinducer-2 follows the expression of an enzyme upstream in the activated methyl cycle and providing its precursor, rather than the expression of its own synthase. Conclusions/Significance Despite sharing the S-adenosylmethionine precursor, no strong link was detected between the production kinetics or metabolic pathways of autoinducers-1 and -2. In contrast, the signaling pathway of autoinducer-2 seems to be switched off by the indole-3-acetic acid pathway under tryptophan control. It therefore appears that the two genera of soft-rot bacteria have similarities but also differences in the

Dynamics of Activated Molecules

Energy Technology Data Exchange (ETDEWEB)

Mullin, Amy S. [Univ. of Maryland, College Park, MD (United States)

2016-11-16

Experimental studies have been performed to investigate the collisional energy transfer processes of gas-phase molecules that contain large amounts of internal energy. Such molecules are prototypes for molecules under high temperature conditions relevant in combustion and information about their energy transfer mechanisms is needed for a detailed understanding and modeling of the chemistry. We use high resolution transient IR absorption spectroscopy to measure the full, nascent product distributions for collisions of small bath molecules that relax highly vibrationally excited pyrazine molecules with E=38000 cm-1 of vibrational energy. To perform these studies, we developed new instrumentation based on modern IR light sources to expand our experimental capabilities to investigate new molecules as collision partners. This final report describes our research in four areas: the characterization of a new transient absorption spectrometer and the results of state-resolved collision studies of pyrazine(E) with HCl, methane and ammonia. Through this research we have gained fundamental new insights into the microscopic details of relatively large complex molecules at high energy as they undergo quenching collisions and redistribute their energy.

Electron-molecule collisions

International Nuclear Information System (INIS)

Shimamura, I.; Takayanagi, K.

1984-01-01

The study of collision processes plays an important research role in modern physics. Many significant discoveries have been made by means of collision experiments. Based on theoretical, experimental, and computational studies, this volume presents an overview detailing the basic processes of electron-molecule collisions. The editors have collected papers-written by a group of international experts-that consider a diverse range of phenomena occurring in electronmolecule collisions. The volume discusses first the basic formulation for scattering problems and then gives an outline of the physics of electron-molecule collisions. The main topics covered are rotational transitions, vibrational transitions, dissociation of molecules in slow collisions, the electron-molecule collision as a spectroscopic tool for studying molecular electronic structures, and experimental and computational techniques for determining the cross sections. These well-referenced chapters are self-contained and can be read independently or consecutively. Authoritative and up-to-date, Electron-Molecule Collisions is a useful addition to the libraries of students and researchers in the fields of atomic, molecular, and chemical physics, and physical chemistry

Powerful effective one-electron Hamiltonian for describing many-atom interacting systems

International Nuclear Information System (INIS)

Lugo, J.O.; Vergara, L.I.; Bolcatto, P.G.; Goldberg, E.C.

2002-01-01

In this paper, we present an alternative way to build the effective one-electron picture of a many-atom interacting system. By simplifying the many-body general problem we present two different options for the bond-pair model Hamiltonian. We have found that the successive approximations in order to achieve the effective description have a dramatic influence on the result. Thus, only the model that introduces the correct renormalization in the diagonal term due to the overlap is able to reproduce, even in a quantitative fashion, the main properties of simple homonuclear diatomic molecules. The success of the model resides in the accurate definitions (free of parametrization) of the Hamiltonian terms, which, therefore, could be used to describe more complex interacting systems such as polyatomic molecules, adsorbed species, or atoms scattered by a surface

Introductory quantum chemistry

International Nuclear Information System (INIS)

Chandra, A.K.

1974-01-01

This book on quantum chemistry is primarily intended for university students at the senior undergraduate level. It serves as an aid to the basic understanding of the important concepts of quantum mechanics introduced in the field of chemistry. Various chapters of the book are devoted to the following : (i) Waves and quanta, (ii) Operator concept in quantum chemistry, (iii) Wave mechanics of some simple systems, (iv) Perturbation theory, (v) Many-electron atoms and angular momenta (vi) Molecular orbital theory and its application to the electronic structure of diatomic molecules, (vii) Chemical bonding in polyatomic molecules and (viii) Chemical applications of Hellmann-Feynman theorem. At the end of each chapter, a set of problems is given and the answers to these problems are given at the end of the book. (A.K.)

Small molecule inhibitors of HCV replication from Pomegranate

Science.gov (United States)

Reddy, B. Uma; Mullick, Ranajoy; Kumar, Anuj; Sudha, Govindarajan; Srinivasan, Narayanaswamy; Das, Saumitra

2014-06-01

Hepatitis C virus (HCV) is the causative agent of end-stage liver disease. Recent advances in the last decade in anti HCV treatment strategies have dramatically increased the viral clearance rate. However, several limitations are still associated, which warrant a great need of novel, safe and selective drugs against HCV infection. Towards this objective, we explored highly potent and selective small molecule inhibitors, the ellagitannins, from the crude extract of Pomegranate (Punica granatum) fruit peel. The pure compounds, punicalagin, punicalin, and ellagic acid isolated from the extract specifically blocked the HCV NS3/4A protease activity in vitro. Structural analysis using computational approach also showed that ligand molecules interact with the catalytic and substrate binding residues of NS3/4A protease, leading to inhibition of the enzyme activity. Further, punicalagin and punicalin significantly reduced the HCV replication in cell culture system. More importantly, these compounds are well tolerated ex vivo and`no observed adverse effect level' (NOAEL) was established upto an acute dose of 5000 mg/kg in BALB/c mice. Additionally, pharmacokinetics study showed that the compounds are bioavailable. Taken together, our study provides a proof-of-concept approach for the potential use of antiviral and non-toxic principle ellagitannins from pomegranate in prevention and control of HCV induced complications.

Studies on the role of unsaturation in the fatty acid surfactant molecule on the thermal conductivity of magnetite nanofluids.

Science.gov (United States)

Lenin, Ramanujam; Joy, Pattayil Alias

2017-11-15

To study the role of unsaturation in the surfactant molecule on the thermal conductivity of magnetite nanofluids, four different fatty acid (stearic, oleic, linoleic, and linolenic acids with different degree of unsaturation) coated magnetite nanoparticles of comparable size are prepared and dispersed in toluene. It is found that the nanofluid with the saturated fatty acid coated nanoparticles show larger viscosity than the fluid with the unsaturated fatty acid coated particles at all concentrations. Thermal conductivity studies show enhancement only above a critical concentration for all fluids. The critical concentration for thermal conductivity enhancement varies with the surfactant, possibly due to the difference in the degree of aggregation of the nanoparticles in the fluid, because of the difference in the conformation of the surfactant molecules on the nanoparticle's surface. The experimental thermal conductivity follows the Maxwell model at higher concentrations. From the overall studies, it is observed that the thermal conductivity of the fluids with aggregated or assembled nanoparticles shows slightly larger enhancement than that of the fluids with isolated particles. However, in the presence of a magnetic field, the fluids with isolated nanoparticles showed relatively larger enhancement, possibly due to the easy response of the isolated magnetite nanoparticles to the applied field. Copyright © 2017 Elsevier Inc. All rights reserved.

Exotic helium molecules; Molecules exotiques d'helium

Energy Technology Data Exchange (ETDEWEB)

Portier, M

2007-12-15

We study the photo-association of an ultracold cloud of magnetically trapped helium atoms: pairs of colliding atoms interact with one or two laser fields to produce a purely long range {sup 4}He{sub 2}(2{sup 3}S{sub 1}-2{sup 3}P{sub 0}) molecule, or a {sup 4}He{sub 2}(2{sup 3}S{sub 1}-2{sup 3}S{sub 1}) long range molecule. Light shifts in one photon photo-association spectra are measured and studied as a function of the laser polarization and intensity, and the vibrational state of the excited molecule. They result from the light-induced coupling between the excited molecule, and bound and scattering states of the interaction between two metastable atoms. Their analysis leads to the determination of the scattering length a = (7.2 {+-} 0.6) ruling collisions between spin polarized atoms. The two photon photo-association spectra show evidence of the production of polarized, long-range {sup 4}He{sub 2}(2{sup 3}S{sub 1}-2{sup 3}S{sub 1}) molecules. They are said to be exotic as they are made of two metastable atoms, each one carrying a enough energy to ionize the other. The corresponding lineshapes are calculated and decomposed in sums and products of Breit-Wigner and Fano profiles associated to one and two photon processes. The experimental spectra are fit, and an intrinsic lifetime {tau} = (1.4 {+-} 0.3) {mu}s is deduced. It is checked whether this lifetime could be limited by spin-dipole induced Penning autoionization. This interpretation requires that there is a quasi-bound state close to the dissociation threshold in the singlet interaction potential between metastable helium atoms for the theory to match the experiment. (author)

Single-molecule mechanics of protein-labelled DNA handles

Directory of Open Access Journals (Sweden)

Vivek S. Jadhav

2016-01-01

Full Text Available DNA handles are often used as spacers and linkers in single-molecule experiments to isolate and tether RNAs, proteins, enzymes and ribozymes, amongst other biomolecules, between surface-modified beads for nanomechanical investigations. Custom DNA handles with varying lengths and chemical end-modifications are readily and reliably synthesized en masse, enabling force spectroscopic measurements with well-defined and long-lasting mechanical characteristics under physiological conditions over a large range of applied forces. Although these chemically tagged DNA handles are widely used, their further individual modification with protein receptors is less common and would allow for additional flexibility in grabbing biomolecules for mechanical measurements. In-depth information on reliable protocols for the synthesis of these DNA–protein hybrids and on their mechanical characteristics under varying physiological conditions are lacking in literature. Here, optical tweezers are used to investigate different protein-labelled DNA handles in a microfluidic environment under different physiological conditions. Digoxigenin (DIG-dsDNA-biotin handles of varying sizes (1000, 3034 and 4056 bp were conjugated with streptavidin or neutravidin proteins. The DIG-modified ends of these hybrids were bound to surface-modified polystyrene (anti-DIG beads. Using different physiological buffers, optical force measurements showed consistent mechanical characteristics with long dissociation times. These protein-modified DNA hybrids were also interconnected in situ with other tethered biotinylated DNA molecules. Electron-multiplying CCD (EMCCD imaging control experiments revealed that quantum dot–streptavidin conjugates at the end of DNA handles remain freely accessible. The experiments presented here demonstrate that handles produced with our protein–DNA labelling procedure are excellent candidates for grasping single molecules exposing tags suitable for molecular

An advanced kinetic theory for morphing continuum with inner structures

Science.gov (United States)

Chen, James

2017-12-01

Advanced kinetic theory with the Boltzmann-Curtiss equation provides a promising tool for polyatomic gas flows, especially for fluid flows containing inner structures, such as turbulence, polyatomic gas flows and others. Although a Hamiltonian-based distribution function was proposed for diatomic gas flow, a general distribution function for the generalized Boltzmann-Curtiss equations and polyatomic gas flow is still out of reach. With assistance from Boltzmann's entropy principle, a generalized Boltzmann-Curtiss distribution for polyatomic gas flow is introduced. The corresponding governing equations at equilibrium state are derived and compared with Eringen's morphing (micropolar) continuum theory derived under the framework of rational continuum thermomechanics. Although rational continuum thermomechanics has the advantages of mathematical rigor and simplicity, the presented statistical kinetic theory approach provides a clear physical picture for what the governing equations represent.

Detecting and characterizing N-acyl-homoserine lactone signal molecules by thin-layer chromatography

Science.gov (United States)

Shaw, Paul D.; Ping, Gao; Daly, Sean L.; Cha, Chung; Cronan, John E.; Rinehart, Kenneth L.; Farrand, Stephen K.

1997-01-01

Many Gram-negative bacteria regulate gene expression in response to their population size by sensing the level of acyl-homoserine lactone signal molecules which they produce and liberate to the environment. We have developed an assay for these signals that couples separation by thin-layer chromatography with detection using Agrobacterium tumefaciens harboring lacZ fused to a gene that is regulated by autoinduction. With the exception of N-butanoyl-l-homoserine lactone, the reporter detected acyl-homoserine lactones with 3-oxo-, 3-hydroxy-, and 3-unsubstituted side chains of all lengths tested. The intensity of the response was proportional to the amount of the signal molecule chromatographed. Each of the 3-oxo- and the 3-unsubstituted derivatives migrated with a unique mobility. Using the assay, we showed that some bacteria produce as many as five detectable signal molecules. Structures could be assigned tentatively on the basis of mobility and spot shape. The dominant species produced by Pseudomonas syringae pv. tabaci chromatographed with the properties of N-(3-oxohexanoyl)-l-homoserine lactone, a structure that was confirmed by mass spectrometry. An isolate of Pseudomonas fluorescens produced five detectable species, three of which had novel chromatographic properties. These were identified as the 3-hydroxy- forms of N-hexanoyl-, N-octanoyl-, and N-decanoyl-l-homoserine lactone. The assay can be used to screen cultures of bacteria for acyl-homoserine lactones, for quantifying the amounts of these molecules produced, and as an analytical and preparative aid in determining the structures of these signal molecules. PMID:9177164

Infrared and Raman study of the fast internal motions of non-rigid molecules in condensed state: method of selective deuteration

International Nuclear Information System (INIS)

Lascombe, J.; Cavagnat, D.; Lassegues, J.C.; Rafilipomanana, C.

1983-01-01

The dynamical behaviour of non-rigid molecules in the gas state is now well known but very little information is available on these molecules in condensed state. The authors present a method of study based on the analysis of the infrared and Raman spectra of selectively deuterated molecules. It is applied to the nitromethane and cyclopentene molecules which provide respectively characteristic examples of methyl internal rotation and ring-puckering motion. In each case, an isolated -C0 or -CD oscillator is modulated by the internal motion and several γ(CH) or γ(CD) bands are observed as a result of the dependence of the vibrational frequency of the oscillator on its conformational situation. Moreover, in the case of crystalline nitromethane a detailed study of the temperature dependence of the band profiles allows the main mechanism of relaxation of the -CH oscillator to be deduced. (orig.)

Isotope separation using vibrationally excited molecules

International Nuclear Information System (INIS)

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

1979-01-01

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

Inter-molecule interaction for magnetic property of vanadyl tetrakis(thiadiazole) porphyrazine film on Au(1 1 1)

Science.gov (United States)

Hou, Jie; Wang, Yu; Eguchi, Keitaro; Nanjo, Chihiro; Takaoka, Tsuyoshi; Sainoo, Yasuyuki; Awaga, Kunio; Komeda, Tadahiro

2018-05-01

We report scanning tunneling microscope (STM) observation of vanadyl tetrakis(thiadiazole) porphyrazine (VOTTDPz) molecules, which is a family molecule of phthalocyanine (Pc) but without Csbnd H termination in the perimeter, deposited on Au(1 1 1) surface. Well-ordered film corresponding to 4 × 4 superstructure with respect to Au(1 1 1) surface is formed, in which the centers of the molecules are separated by 1.12 nm, which is much smaller than that observed for a VOPc molecule on Au(1 1 1), due to the absence of Csbnd H termination. At the same time, the azimuthal angles of neighboring molecules rotate with each other by 30°. A contrast variation of bright and dark molecules is observed, which are interpreted as O-up and O-down molecules, respectively, based on the density functional theory simulation. Spin-polarized local density of states calculation shows spin-polarized V 3d state, which is delocalized over the ring. Spin detection is executed by measuring Kondo resonance in the tunneling spectroscopy near the Fermi level, which is caused by the interaction of an isolated spin and conduction electron of the substrate. We detected asymmetric and weak Kondo peak for out-of-plane outer magnetic field of 0 T, which becomes strong and symmetric peak at 5 T, which is understood by the shift of the spin center of the Kondo resonance from V 3d to delocalized π state in ring with the magnetic field.

Selective excitation, relaxation, and energy channeling in molecular systems

International Nuclear Information System (INIS)

Rhodes, W.C.

1993-08-01

Research involves theoretical studies of response, relaxation, and correlated motion in time-dependent behavior of large molecular systems ranging from polyatomic molecules to protein molecules in their natural environment. Underlying theme is subsystem modulation dynamics. Main idea is that quantum mechanical correlations between components of a system develop with time, playing a major role in determining the balance between coherent and dissipative forces. Central theme is interplay of coherence and dissipation in determining the nature of dynamic structuring and energy flow in molecular transformation mechanisms. Subsystem equations of motion are being developed to show how nonlinear, dissipative dynamics of a particular subsystem arise from correlated interactions with the rest of the system (substituent groups, solvent, lattice modes, etc.); one consequence is resonance structures and networks. Quantum dynamics and thermodynamics are being applied to understand control and energy transfer mechanisms in biological functions of protein molecules; these mechanisms are both global and local. Besides the above theory, the research deals with phenomenological aspects of molecular systems

Direct Visualization of Valence Electron Motion Using Strong-Field Photoelectron Holography

Science.gov (United States)

He, Mingrui; Li, Yang; Zhou, Yueming; Li, Min; Cao, Wei; Lu, Peixiang

2018-03-01

Watching the valence electron move in molecules on its intrinsic timescale has been one of the central goals of attosecond science and it requires measurements with subatomic spatial and attosecond temporal resolutions. The time-resolved photoelectron holography in strong-field tunneling ionization holds the promise to access this realm. However, it remains to be a challenging task hitherto. Here we reveal how the information of valence electron motion is encoded in the hologram of the photoelectron momentum distribution (PEMD) and develop a novel approach of retrieval. As a demonstration, applying it to the PEMDs obtained by solving the time-dependent Schrödinger equation for the prototypical molecule H2+ , the attosecond charge migration is directly visualized with picometer spatial and attosecond temporal resolutions. Our method represents a general approach for monitoring attosecond charge migration in more complex polyatomic and biological molecules, which is one of the central tasks in the newly emerging attosecond chemistry.

Molecular beam studies of reaction dynamics

International Nuclear Information System (INIS)

Lee, Yuan T.

1991-03-01

The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation

Molecular beam studies of reaction dynamics

Energy Technology Data Exchange (ETDEWEB)

Lee, Y.T. [Lawrence Berkeley Laboratory, CA (United States)

1993-12-01

The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.

Effect of deuteration on the vibrational spectra of organic molecules

International Nuclear Information System (INIS)

Billes, Ferenc; Endredi, Henrietta; Varady, Balazs

2001-01-01

The stable isotope substitution of organic compounds deforms their vibrational spectra. The modifications of the spectra appear as band shifts and changes in intensities and shapes of the bands. The magnitude of the effect depends on the ratio of the masses of the new and old isotopes and on the atom active position. According to these mentioned reasons large effects can be observed only if hydrogen atoms are substituted. With the effect of the substitution we dealt already in a former lecture. In this lecture we concentrate on the effect of the change of hydrogen to deuterium. We investigate the changes both experimentally and theoretically. There are two possibilities: - the hydrogen atom is in an active position, its interaction with the environment is strong, either it can dissociate or move on the skeleton of the molecule (tautomerism, resonance) and it can build hydrogen bond, (e.g. it is connected to nitrogen and oxygen atoms); - the hydrogen atom is in an indifferent position in the molecule, its interaction with the environment is weak (e.g. it joins carbon atom). When building the hydrogen bond besides the hydrogen donors also acceptors exist, namely, oxygen and nitrogen atoms having non-bonded electron pairs. When comparing the experimental and theoretical (calculated) effects of this type of isotope changes one must take into account that the calculations refer to the isolated molecule while the experimental spectra characterize the compound. The hydrogen bond is a very strong intermolecular interaction and produces tremendous changes in the infrared spectrum of the molecule in comparison to the imagined theoretical spectrum of the molecule. Some bands disappear, appear, or shift and deform drastically. The H/D change diminishes these effects. Of course, these changes entail the shift of several bands. The Raman spectrum is less sensitive to the large dipole moment changes therefore the deuteration effect is there less dramatic. Deuteration of hydrogen

Single-Molecule Spectroscopy

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 20; Issue 2. Single-Molecule Spectroscopy: Every Molecule is Different! Kankan Bhattacharyya. General Article Volume 20 Issue 2 February 2015 pp 151-164. Fulltext. Click here to view fulltext PDF. Permanent link:

Photochemical activation and reactivity of polynuclear transition metal complex molecules. Final report

International Nuclear Information System (INIS)

Endicott, J.F.; Lintvedt, R.L.

1982-06-01

Several bi- and trinuclear metal complexes containing ligands from β-polyketonates have been synthesized and characterized including homo- and hetero-polynuclear complexes. New synthetic approaches to the preparation of heterobi- and trinuclear complexes have been developed that allow the preparation of a large number of molecules containing heavy-metal ions such as Pd 2+ or UO 2 2+ and a first-row transition-metal ion. The electrochemical properties of these complexes have been investigated and many exhibit the ability to transfer two electrons at very nearly the same potential. Photochemical studies on binuclear Cu(II) and Ni(II) showed that these compounds yielded reduced metal species and decomposition upon irradiation. Luminescence of hetero-complexes of uranyl polyketonates is observed at 77 0 K with the UO 2 2+ moiety functioning as an isolated chromophore in which emission is observed only on direct excitation of UO 2 2+ and energy transfer to lower states in the molecule is not observed

Coupled-cluster treatment of molecular strong-field ionization

Science.gov (United States)

Jagau, Thomas-C.

2018-05-01

Ionization rates and Stark shifts of H2, CO, O2, H2O, and CH4 in static electric fields have been computed with coupled-cluster methods in a basis set of atom-centered Gaussian functions with a complex-scaled exponent. Consideration of electron correlation is found to be of great importance even for a qualitatively correct description of the dependence of ionization rates and Stark shifts on the strength and orientation of the external field. The analysis of the second moments of the molecular charge distribution suggests a simple criterion for distinguishing tunnel and barrier suppression ionization in polyatomic molecules.

Ion-Molecule Reaction Dynamics.

Science.gov (United States)

Meyer, Jennifer; Wester, Roland

2017-05-05

We review the recent advances in the investigation of the dynamics of ion-molecule reactions. During the past decade, the combination of single-collision experiments in crossed ion and neutral beams with the velocity map ion imaging detection technique has enabled a wealth of studies on ion-molecule reactions. These methods, in combination with chemical dynamics simulations, have uncovered new and unexpected reaction mechanisms, such as the roundabout mechanism and the subtle influence of the leaving group in anion-molecule nucleophilic substitution reactions. For this important class of reactions, as well as for many fundamental cation-molecule reactions, the information obtained with crossed-beam imaging is discussed. The first steps toward understanding micro-solvation of ion-molecule reaction dynamics are presented. We conclude with the presentation of several interesting directions for future research.

Velocity effect on aptamer-based circulating tumor cell isolation in microfluidic devices.

Science.gov (United States)

Wan, Yuan; Tan, Jifu; Asghar, Waseem; Kim, Young-tae; Liu, Yaling; Iqbal, Samir M

2011-12-01

The isolation and detection of rare circulating tumor cells (CTCs) has been one of the focuses of intense research recently. In a microfluidic device, a number of factors can influence the enrichment capability of surface-bound probe molecules. This article analyzes the important factor of flow velocity in a microfluidic channel. The competition of surface-grafted anti-EGFR aptamers to bind the overexpressed EGFR on cell membranes against the drag force from the fluid flow is an important efficiency determining factor. The flow rate variations are applied both in experiments and in simulation models to study their effects on CTC capture efficiency. A mixture of mononuclear cells and human Glioblastoma cells is used to isolate cancer cells from the cellular flow. The results show interdependence between the adhesion probability, isolation efficiency, and flow rate. This work can help in designing flow-through lab-on-chip devices that use surface-bound probe affinities against overexpressed biomarkers for cell isolation. This work demonstrates that microfluidic based approaches have strong potential applications in CTC detection and isolation. © 2011 American Chemical Society

Cyclophilin C Participates in the US2-Mediated Degradation of Major Histocompatibility Complex Class I Molecules.

Science.gov (United States)

Chapman, Daniel C; Stocki, Pawel; Williams, David B

2015-01-01

Human cytomegalovirus uses a variety of mechanisms to evade immune recognition through major histocompatibility complex class I molecules. One mechanism mediated by the immunoevasin protein US2 causes rapid disposal of newly synthesized class I molecules by the endoplasmic reticulum-associated degradation pathway. Although several components of this degradation pathway have been identified, there are still questions concerning how US2 targets class I molecules for degradation. In this study we identify cyclophilin C, a peptidyl prolyl isomerase of the endoplasmic reticulum, as a component of US2-mediated immune evasion. Cyclophilin C could be co-isolated with US2 and with the class I molecule HLA-A2. Furthermore, it was required at a particular expression level since depletion or overexpression of cyclophilin C impaired the degradation of class I molecules. To better characterize the involvement of cyclophilin C in class I degradation, we used LC-MS/MS to detect US2-interacting proteins that were influenced by cyclophilin C expression levels. We identified malectin, PDIA6, and TMEM33 as proteins that increased in association with US2 upon cyclophilin C knockdown. In subsequent validation all were shown to play a functional role in US2 degradation of class I molecules. This was specific to US2 rather than general ER-associated degradation since depletion of these proteins did not impede the degradation of a misfolded substrate, the null Hong Kong variant of α1-antitrypsin.

Electron Accumulative Molecules.

Science.gov (United States)

Buades, Ana B; Sanchez Arderiu, Víctor; Olid-Britos, David; Viñas, Clara; Sillanpää, Reijo; Haukka, Matti; Fontrodona, Xavier; Paradinas, Markos; Ocal, Carmen; Teixidor, Francesc

2018-02-28

With the goal to produce molecules with high electron accepting capacity and low reorganization energy upon gaining one or more electrons, a synthesis procedure leading to the formation of a B-N(aromatic) bond in a cluster has been developed. The research was focused on the development of a molecular structure able to accept and release a specific number of electrons without decomposing or change in its structural arrangement. The synthetic procedure consists of a parallel decomposition reaction to generate a reactive electrophile and a synthesis reaction to generate the B-N(aromatic) bond. This procedure has paved the way to produce the metallacarboranylviologen [M(C 2 B 9 H 11 )(C 2 B 9 H 10 )-NC 5 H 4 -C 5 H 4 N-M'(C 2 B 9 H 11 )(C 2 B 9 H 10 )] (M = M' = Co, Fe and M = Co and M' = Fe) and semi(metallacarboranyl)viologen [3,3'-M(8-(NC 5 H 4 -C 5 H 4 N-1,2-C 2 B 9 H 10 )(1',2'-C 2 B 9 H 11 )] (M = Co, Fe) electron cumulative molecules. These molecules are able to accept up to five electrons and to donate one in single electron steps at accessible potentials and in a reversible way. By targeted synthesis and corresponding electrochemical tests each electron transfer (ET) step has been assigned to specific fragments of the molecules. The molecules have been carefully characterized, and the electronic communication between both metal centers (when this situation applies) has been definitely observed through the coplanarity of both pyridine fragments. The structural characteristics of these molecules imply a low reorganization energy that is a necessary requirement for low energy ET processes. This makes them electronically comparable to fullerenes, but on their side, they have a wide range of possible solvents. The ET from one molecule to another has been clearly demonstrated as well as their self-organizing capacity. We consider that these molecules, thanks to their easy synthesis, ET, self-organizing capacity, wide range of solubility, and easy processability, can

Single molecule conductance

NARCIS (Netherlands)

Willems, R.

2008-01-01

This thesis represents an excursion into the world of molecular electronics, i.e. the field of research trying to use individual (organic) molecules as electronic components; in this work various experimental methods have been explored to connect individual molecules to metallic contacts and

The Molecule Cloud - compact visualization of large collections of molecules

Directory of Open Access Journals (Sweden)

Ertl Peter

2012-07-01

Full Text Available Abstract Background Analysis and visualization of large collections of molecules is one of the most frequent challenges cheminformatics experts in pharmaceutical industry are facing. Various sophisticated methods are available to perform this task, including clustering, dimensionality reduction or scaffold frequency analysis. In any case, however, viewing and analyzing large tables with molecular structures is necessary. We present a new visualization technique, providing basic information about the composition of molecular data sets at a single glance. Summary A method is presented here allowing visual representation of the most common structural features of chemical databases in a form of a cloud diagram. The frequency of molecules containing particular substructure is indicated by the size of respective structural image. The method is useful to quickly perceive the most prominent structural features present in the data set. This approach was inspired by popular word cloud diagrams that are used to visualize textual information in a compact form. Therefore we call this approach “Molecule Cloud”. The method also supports visualization of additional information, for example biological activity of molecules containing this scaffold or the protein target class typical for particular scaffolds, by color coding. Detailed description of the algorithm is provided, allowing easy implementation of the method by any cheminformatics toolkit. The layout algorithm is available as open source Java code. Conclusions Visualization of large molecular data sets using the Molecule Cloud approach allows scientists to get information about the composition of molecular databases and their most frequent structural features easily. The method may be used in the areas where analysis of large molecular collections is needed, for example processing of high throughput screening results, virtual screening or compound purchasing. Several example visualizations of large

Immersion Refractometry of Isolated Bacterial Cell Walls

Science.gov (United States)

Marquis, Robert E.

1973-01-01

Immersion-refractometric and light-scattering measurements were adapted to determinations of average refractive indices and physical compactness of isolated bacterial cell walls. The structures were immersed in solutions containing various concentrations of polymer molecules that cannot penetrate into wall pores, and then an estimate was made of the polymer concentration or the refractive index of the polymer solution in which light scattering was reduced to zero. Because each wall preparation was heterogeneous, the refractive index of the medium for zero light scattering had to be estimated by extrapolation. Refractive indices for walls suspended in bovine serum albumin solutions ranged from 1.348 for walls of the rod form of Arthrobacter crystallopoietes to 1.382 for walls of the teichoic acid deficient, 52A5 strain of Staphylococcus aureus. These indices were used to calculate approximate values for solids content per milliliter, and the calculated values agreed closely with those estimated from a knowledge of dextran-impermeable volumes per gram, dry weight, of the walls. When large molecules such as dextrans or serum albumin were used for immersion refractometry, the refractive indices obtained were for entire walls, including both wall polymers and wall water. When smaller molecules that can penetrate wall pores to various extents were used with Micrococcus lysodeikticus walls, the average, apparent refractive index of the structures increased as the molecular size of probing molecules was decreased. It was possible to obtain an estimate of 1.45 to 1.46 for the refractive index of wall polymers, predominantly peptidoglycans in this case, by extrapolating the curve for refractive index versus molecular radius to a value of 0.2 nm, the approximate radius of a water molecule. This relatively low value for polymer refractive index was interpreted as evidence in favor of the amorphous, elastic model of peptidoglycan structure and against the crystalline, rigid

Helium atoms and molecules in strong magnetic fields

Science.gov (United States)

Mori, K.

Recent theoretical studies have shown that the neutron star surface may be composed of helium or heavier elements as hydrogen may be quickly depleted by diffuse nuclear burning Chang Bildsten However while Hydrogen atmospheres have been studied in great details atomic data for helium is available only for He ion Pavlov Bezchastnov 2005 We performed Hartree-Fock type calculation for Helium atom and molecules and computed their binding ionization and dissociation energies in strong magnetic fields B sim10 12 -- 10 15 G We will present ionization balance of Helium atmospheres at typical magnetic field strengths and temperatures to radio-quiet neutron stars and AXPs We will also discuss several implications of helium atmosphere to X-ray data of isolated neutron stars focusing on the detected spectral features

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

Science.gov (United States)

Enoki, Toshiaki; Kiguchi, Manabu

2018-03-01

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

Energy transfer in isolated LHC II studied by femtosecond pump-probe technique

CERN Document Server

Yang Yi; Liu Yuan; Liu Wei Min; Zhu Rong Yi; Qian Shi Xiong; Xu Chun He

2003-01-01

Excitation energy transfer in the isolated light-harvesting chlorophyll (Chl)-a/b protein complex of photosystem II (LHC II) was studied by the one-colour pump-probe technique with femtosecond time resolution. After exciting Chl-b by 638nm beam, the dynamic behaviour shows that the ultrafast energy transfer from Chl-b at positions of B2, B3, and B5 to the corresponding Chl-a molecules in monomeric subunit of LHC II is in the time scale of 230fs. While with the excitation of Chl-a at 678nm, the energy transfer between excitons of Chl-a molecules has the lifetime of about 370 fs, and two other slow decay components are due to the energy transfer between different Chl-a molecules in a monomeric subunit of LHC II or in different subunits, or due to change of molecular conformation. (20 refs).

Electron-molecule collisions

CERN Document Server

Takayanagi, Kazuo

1984-01-01

Scattering phenomena play an important role in modern physics. Many significant discoveries have been made through collision experiments. Amongst diverse kinds of collision systems, this book sheds light on the collision of an electron with a molecule. The electron-molecule collision provides a basic scattering problem. It is scattering by a nonspherical, multicentered composite particle with its centers having degrees of freedom of motion. The molecule can even disintegrate, Le., dissociate or ionize into fragments, some or all of which may also be molecules. Although it is a difficult problem, the recent theoretical, experimental, and computational progress has been so significant as to warrant publication of a book that specializes in this field. The progress owes partly to technical develop­ ments in measurements and computations. No less important has been the great and continuing stimulus from such fields of application as astrophysics, the physics of the earth's upper atmosphere, laser physics, radiat...

Preparation of translationally cold neutral molecules.

Science.gov (United States)

Di Domenicantonio, Giulia; Bertsche, Benjamin; Osterwalder, Andreas

2011-01-01

Efforts at EPFL to obtain translationally cold neutral molecules are described. Active deceleration of polar molecules is performed by confining the molecules in moving three-dimensional electrostatic traps, and by appropriately choosing the velocity of those traps. Alternatively, cold molecules can be obtained by velocity filtering. Here, the velocity of the molecules is not changed, but instead the cold molecules are extracted from a thermal sample by using the competition between the electrostatic force and the centrifugal force inside a bent electrostatic guide for polar molecules.

Isolation and characterization of 20'-F-RNA aptamers against whole HIV-1 subtype C envelope pseudovirus

CSIR Research Space (South Africa)

London, GM

2015-01-01

Full Text Available Aptamers, which are artificial nucleic acid ligands akin to antibodies in function, represent a new class of molecules that can prevent HIV infection. In this study, we isolated RNA aptamers against whole HV-1CAP45 enveloped pseudotyped virus...

Matrix Isolation Spectroscopy of H2O2, D2O, and HDO in Solid Parahydrogen

National Research Council Canada - National Science Library

Fajardo, Mario

2003-01-01

...) solids doped with H2O, D2O and HDO molecules. Analysis of the rovibrational spectra of the isolated H20, D2O and HDO monomers reveals their existence as very slightly hindered rotors, typically showing only 2 to 5...

Single-Molecule Electronics with Cross- Conjugated Molecules: Quantum Interference, IETS and Non-Equilibrium "Temperatures"

DEFF Research Database (Denmark)

Jørgensen, Jacob Lykkebo

Abstract The idea of using single-molecules as components in electronic devices is fas- cinating. For this idea to come into fruition, a number of technical and theo- retical challenges must be overcome. In this PhD thesis, the electron-phonon interaction is studied for a special class of molecules......, which is characterised by destructive quantum interference. The molecules are cross-conjugated, which means that the two parts of the molecules are conjugated to a third part, but not to each other. This gives rise to an anti-resonance in the trans- mission. In the low bias and low temperature regime......-conjugated molecules. We nd that the vibrational modes that would be expected to dominate, following the propensity, rules are very weak. Instead, other modes are found to be the dominant ones. We study this phenomenon for a number of cross-conjugated molecules, and link these ndings to the anti...

Single Molecule Electronics and Devices

Science.gov (United States)

Tsutsui, Makusu; Taniguchi, Masateru

2012-01-01

The manufacture of integrated circuits with single-molecule building blocks is a goal of molecular electronics. While research in the past has been limited to bulk experiments on self-assembled monolayers, advances in technology have now enabled us to fabricate single-molecule junctions. This has led to significant progress in understanding electron transport in molecular systems at the single-molecule level and the concomitant emergence of new device concepts. Here, we review recent developments in this field. We summarize the methods currently used to form metal-molecule-metal structures and some single-molecule techniques essential for characterizing molecular junctions such as inelastic electron tunnelling spectroscopy. We then highlight several important achievements, including demonstration of single-molecule diodes, transistors, and switches that make use of electrical, photo, and mechanical stimulation to control the electron transport. We also discuss intriguing issues to be addressed further in the future such as heat and thermoelectric transport in an individual molecule. PMID:22969345

Isolation and Spectroscopic Characterization of Reactive Species in Atmospheric and Interstellar Reactions

Science.gov (United States)

Relph, Rachael A.

2011-12-01

A critical element to the study of chemical reactions is the characterization of reaction intermediates. Methods have been developed to isolate these transient species in the gas phase and when combined with infrared spectroscopy have proven to be excellent tools for determining the structure and reactivity of key intermediates. The studies presented here exploit these technologies to better understand the chemistry of species involved in atmospheric and interstellar reactions. An excellent example of their utility is in the study of the formation of proton hydrates and HONO in the upper atmosphere by sequential addition of water molecules onto the nitrosonium ion. This reaction only proceeds to products after addition of the fourth water molecule, and isolation and characterization of the intermediate trihydrate, NO+(H 2O)3, shows that this species is formed in three isomeric forms, each with a different water network that controls the degree of bond formation between the nitrosonium ion and an activated water molecule. Many isomeric structures are also seen in the clustering reactions of acetylene which may be a mechanism for the formation of benzene cation in interstellar space. The spectroscopy of the trimer, (C2H2)3 + indicates that this species exists in two major isomer classes; covalent forms, one of which may be benzene, and an ion-molecule complex, comprised of a loosely bound acetylene on a dimer core. Interestingly, this dimer core is different from the cyclobutadiene-like structure observed in dimerized acetylene, and proves to be a robust species on the potential energy surface as it survives further clustering events. Two structural isomers of CO3 -and NO3 - are also investigated, and found to have drastically different infrared spectra which are analyzed in the context of their electronic structure. Isomers in these systems are prepared under different expansion conditions which accounts for their unique spectral signatures.

Isolation and in silico evaluation of antidiabetic molecules of Cynodon dactylon (L.).

Science.gov (United States)

Annapurna, Hasthi V; Apoorva, Babu; Ravichandran, Natesan; Arun, Kallur Purushothaman; Brindha, Pemaiah; Swaminathan, Sethuraman; Vijayalakshmi, Mahadevan; Nagarajan, Arumugam

2013-02-01

Cynodon dactylon is a potential source of metabolites such as flavanoids, alkaloids, glycosides and β-sitosterol and has been traditionally employed to treat urinary tract and other microbial infections and dysentery. The present work attempts to evaluate the activity of C. dactylon extracts for glycemic control. Aqueous extracts of C. dactylon analyzed by HPLC-ESI MS have identified the presence of apigenin, luteolin, 6-C-pentosyl-8-C-hexosyl apigenin and 6-C-hexosyl-8-C-pentosyl luteolin. Evaluation of hypoglycemic activity through an extensive in silico docking approach with PPARγ (Peroxisome Proliferator-Activated Receptor), GLUT-4 (glucose transporter-4) and SGLT2 (sodium glucose co-transporter-2) revealed that luteolin, apigenin, 6-C-pentosyl-8-C-hexosyl apigenin, 6-C-hexosyl-8-C-pentosyl luteolin interact with SGLT2. Interactions of these molecules with Gln 295 and Asp 294 residues of SGLT2 have been shown to compare well with that of the phase III drug, dapagliflozin. These residues have been proven to be responsible for sugar sensing and transport. This work establishes C. dactylon extract as a potential SGLT2 inhibitor for diabetic neuropathy thus enabling a possibility of this plant extract as a new alternative to existing diabetic approaches. Copyright © 2012 Elsevier Inc. All rights reserved.

Small-molecule quinolinol inhibitor identified provides protection against BoNT/A in mice.

Directory of Open Access Journals (Sweden)

Padma Singh

Full Text Available Botulinum neurotoxins (BoNTs, etiological agents of the life threatening neuroparalytic disease botulism, are the most toxic substances currently known. The potential for the use as bioweapon makes the development of small-molecule inhibitor against these deadly toxins is a top priority. Currently, there are no approved pharmacological treatments for BoNT intoxication. Although an effective vaccine/immunotherapy is available for immuno-prophylaxis but this cannot reverse the effects of toxin inside neurons. A small-molecule pharmacological intervention, especially one that would be effective against the light chain protease, would be highly desirable. Similarity search was carried out from ChemBridge and NSC libraries to the hit (7-(phenyl(8-quinolinylaminomethyl-8-quinolinol; NSC 84096 to mine its analogs. Several hits obtained were screened for in silico inhibition using AutoDock 4.1 and 19 new molecules selected based on binding energy and Ki. Among these, eleven quinolinol derivatives potently inhibited in vitro endopeptidase activity of botulinum neurotoxin type A light chain (rBoNT/A-LC on synaptosomes isolated from rat brain which simulate the in vivo system. Five of these inhibitor molecules exhibited IC(50 values ranging from 3.0 nM to 10.0 µM. NSC 84087 is the most potent inhibitor reported so far, found to be a promising lead for therapeutic development, as it exhibits no toxicity, and is able to protect animals from pre and post challenge of botulinum neurotoxin type A (BoNT/A.

Crystal structure of a bioactive sesquiterpene isolated from Artemisia reticulata

Directory of Open Access Journals (Sweden)

A. K. Bauri

2016-04-01

Full Text Available The title compound, C15H24O2 {systematic name: 1-[6-hydroxy-7-(propan-2-yl-4-methylidene-2,3,3a,4,5,6,7,7a-octahydro-1H-inden-1-yl]ethanone} was isolated from A. reticulata by column chromatography over silica gel by gradient solvent elution. The molecule comprises a bicyclo[4.3.0]nonane ring bearing acetoxy, hydroxy and isopropyl substituents, and an exocyclic double bond on the cyclohexane ring. In the bicyclic skeleton, the cyclohexane ring adopts a chair conformation ring and the cyclopentane ring is in an envelope conformation. In the crystal, molecules are linked by O—H...O hydrogen bonds, forming chains along [010]. These chains are cross-linked by C—H...O hydrogen bonds.

A novel small molecule inhibitor of hepatitis C virus entry.

Directory of Open Access Journals (Sweden)

Carl J Baldick

Full Text Available Small molecule inhibitors of hepatitis C virus (HCV are being developed to complement or replace treatments with pegylated interferons and ribavirin, which have poor response rates and significant side effects. Resistance to these inhibitors emerges rapidly in the clinic, suggesting that successful therapy will involve combination therapy with multiple inhibitors of different targets. The entry process of HCV into hepatocytes represents another series of potential targets for therapeutic intervention, involving viral structural proteins that have not been extensively explored due to experimental limitations. To discover HCV entry inhibitors, we utilized HCV pseudoparticles (HCVpp incorporating E1-E2 envelope proteins from a genotype 1b clinical isolate. Screening of a small molecule library identified a potent HCV-specific triazine inhibitor, EI-1. A series of HCVpp with E1-E2 sequences from various HCV isolates was used to show activity against all genotype 1a and 1b HCVpp tested, with median EC50 values of 0.134 and 0.027 µM, respectively. Time-of-addition experiments demonstrated a block in HCVpp entry, downstream of initial attachment to the cell surface, and prior to or concomitant with bafilomycin inhibition of endosomal acidification. EI-1 was equally active against cell-culture adapted HCV (HCVcc, blocking both cell-free entry and cell-to-cell transmission of virus. HCVcc with high-level resistance to EI-1 was selected by sequential passage in the presence of inhibitor, and resistance was shown to be conferred by changes to residue 719 in the carboxy-terminal transmembrane anchor region of E2, implicating this envelope protein in EI-1 susceptibility. Combinations of EI-1 with interferon, or inhibitors of NS3 or NS5A, resulted in additive to synergistic activity. These results suggest that inhibitors of HCV entry could be added to replication inhibitors and interferons already in development.

EDITORIAL: Focus on Cold and Ultracold Molecules FOCUS ON COLD AND ULTRACOLD MOLECULES

Science.gov (United States)

Carr, Lincoln D.; Ye, Jun

2009-05-01

Cold and ultracold molecules are the next wave of ultracold physics, giving rise to an exciting array of scientific opportunities, including many body physics for novel quantum phase transitions, new states of matter, and quantum information processing. Precision tests of fundamental physical laws benefit from the existence of molecular internal structure with exquisite control. The study of novel collision and reaction dynamics will open a new chapter of quantum chemistry. Cold molecules bring together researchers from a variety of fields, including atomic, molecular, and optical physics, chemistry and chemical physics, quantum information science and quantum simulations, condensed matter physics, nuclear physics, and astrophysics, a truly remarkable synergy of scientific explorations. For the past decade there have been steady advances in direct cooling techniques, from buffer-gas cooling to cold molecular beams to electro- and magneto-molecular decelerators. These techniques have allowed a large variety of molecules to be cooled for pioneering studies. Recent amazing advances in experimental techniques combining the ultracold and the ultraprecise have furthermore brought molecules to the point of quantum degeneracy. These latter indirect cooling techniques magnetically associate atoms from a Bose-Einstein condensate and/or a quantum degenerate Fermi gas, transferring at 90% efficiency highly excited Fano-Feshbach molecules, which are on the order of 10 000 Bohr radii in size, to absolute ground state molecules just a few Bohr across. It was this latter advance, together with significant breakthroughs in internal state manipulations, which inspired us to coordinate this focus issue now, and is the reason why we say the next wave of ultracold physics has now arrived. Whether directly or indirectly cooled, heteronuclear polar molecules offer distinct new features in comparison to cold atoms, while sharing all of their advantages (purity, high coherence

Matrix-isolation studies on alkali-metal phosphates

International Nuclear Information System (INIS)

Jenny, S.N.; Ogden, J.S.

1979-01-01

This paper describes the results of a matrix-isolation i.r. study on the vaporisation of trisodium orthophosphate. When this material is heated in vacuo to ca. 1600 K, and the products condensed in a low-temperature argon matrix, the i.r. spectrum obtained is shown to be due to a trapped species NaPO 3 . With the aid of 18 O-enrichment, this molecule is shown to have a Csub(2v) bidentate structure with characteristic i.r. bands at 1 341.7, 1 211.1, 1 004.0, 536.6, 474.0 and 287.0 cm -1 . (author)

Single-Molecule Photocurrent at a Metal-Molecule-Semiconductor Junction.

Science.gov (United States)

Vezzoli, Andrea; Brooke, Richard J; Higgins, Simon J; Schwarzacher, Walther; Nichols, Richard J

2017-11-08

We demonstrate here a new concept for a metal-molecule-semiconductor nanodevice employing Au and GaAs contacts that acts as a photodiode. Current-voltage traces for such junctions are recorded using a STM, and the "blinking" or "I(t)" method is used to record electrical behavior at the single-molecule level in the dark and under illumination, with both low and highly doped GaAs samples and with two different types of molecular bridge: nonconjugated pentanedithiol and the more conjugated 1,4-phenylene(dimethanethiol). Junctions with highly doped GaAs show poor rectification in the dark and a low photocurrent, while junctions with low doped GaAs show particularly high rectification ratios in the dark (>10 3 for a 1.5 V bias potential) and a high photocurrent in reverse bias. In low doped GaAs, the greater thickness of the depletion layer not only reduces the reverse bias leakage current, but also increases the volume that contributes to the photocurrent, an effect amplified by the point contact geometry of the junction. Furthermore, since photogenerated holes tunnel to the metal electrode assisted by the HOMO of the molecular bridge, the choice of the latter has a strong influence on both the steady state and transient metal-molecule-semiconductor photodiode response. The control of junction current via photogenerated charge carriers adds new functionality to single-molecule nanodevices.

Simultaneous infrared and UV-visible absorption spectra of matrix-isolated carbon vapor

Science.gov (United States)

Kurtz, Joe; Huffman, Donald R.

1989-01-01

Carbon molecules were suggested as possible carriers of the diffuse interstellar bands. In particular, it was proposed that the 443 nm diffuse interstellar band is due to the same molecule which gives rise to the 447 nm absorption feature in argon matrix-isolated carbon vapor. If so, then an associated C-C stretching mode should be seen in the IR. By doing spectroscopy in both the IR and UV-visible regions on the same sample, the present work provides evidence for correlating UV-visible absorption features with those found in the IR. Early data indicates no correlation between the strongest IR feature (1997/cm) and the 447 nm band. Correlation with weaker IR features is being investigated.

Adhesion molecules

CERN Document Server

Preedy, Victor R

2016-01-01

This book covers the structure and classification of adhesion molecules in relation to signaling pathways and gene expression. It discusses immunohistochemical localization, neutrophil migration, and junctional, functional, and inflammatory adhesion molecules in pathologies such as leukocyte decompression sickness and ischemia reperfusion injury. Highlighting the medical applications of current research, chapters cover diabetes, obesity, and metabolic syndrome; hypoxia; kidney disease; smoking, atrial fibrillation, and heart disease, the brain and dementia; and tumor proliferation. Finally, it looks at molecular imaging and bioinformatics, high-throughput technologies, and chemotherapy.

Highly Accurate and Precise Infrared Transition Frequencies of the H_3^+ Cation

Science.gov (United States)

Perry, Adam J.; Markus, Charles R.; Hodges, James N.; Kocheril, G. Stephen; McCall, Benjamin J.

2016-06-01

Calculation of ab initio potential energy surfaces for molecules to high accuracy is only manageable for a handful of molecular systems. Among them is the simplest polyatomic molecule, the H_3^+ cation. In order to achieve a high degree of accuracy (Diniz, J.R. Mohallem, A. Alijah, M. Pavanello, L. Adamowicz, O.L. Polyansky, J. Tennyson Phys. Rev. A (2013), 88, 032506 O.L. Polyansky, A. Alijah, N.F. Zobov, I.I. Mizus, R.I. Ovsyannikov, J. Tennyson, L. Lodi, T. Szidarovszky, A.G. Császár Phil. Trans. R. Soc. A (2012), 370, 5014 J.N. Hodges, A.J. Perry, P.A. Jenkins II, B.M. Siller, B.J. McCall J. Chem. Phys. (2013), 139, 164201 A.J. Perry, J.N. Hodges, C.R. Markus, G.S. Kocheril, B.J. McCall J. Molec. Spectrosc. (2015), 317, 71-73.

Nonunique and nonuniform mapping in few-body Coulomb-explosion imaging

Science.gov (United States)

Sayler, A. M.; Eckner, E.; McKenna, J.; Esry, B. D.; Carnes, K. D.; Ben-Itzhak, I.; Paulus, G. G.

2018-03-01

Much of our knowledge of molecular geometry and interaction dynamics comes from indirect measurements of the molecular fragments following breakup. This technique—Coulomb-explosion imaging (CEI), i.e., determining the initial molecular configuration of a system from the momenta of the resulting fragments using knowledge of the particle interactions—is one of the fundamental tools of molecular physics. Moreover, CEI has been a staple of molecular studies for decades. Here we show that one often cannot assign a unique initial configuration to the few-body breakup of a polyatomic molecule given the measurement of the resulting fragments' momenta. Specifically, multiple initial configurations can result in identical momenta for a molecule breaking into three or more parts. Further, the nonunique and nonuniform mapping from the initial configuration to the measured momenta also significantly complicates the determination of molecular alignment at the time of breakup.

Stability of matter-antimatter molecules

International Nuclear Information System (INIS)

Wong, Cheuk-Yin; Lee, Teck-Ghee

2011-01-01

Highlights: → We examine stability of matter-antimatter molecules with four constituents. → The binding of matter-antimatter molecules is a common phenomenon. → Molecules have bound states if ratio of constituent masses greater than ∼4. → We evaluate molecular binding energies and annihilation lifetimes. - Abstract: We examine the stability of matter-antimatter molecules by reducing the four-body problem into a simpler two-body problem with residual interactions. We find that matter-antimatter molecules with constituents (m 1 + ,m 2 - ,m-bar 2 + ,m-bar 1 - ) possess bound states if their constituent mass ratio m 1 /m 2 is greater than about 4. This stability condition suggests that the binding of matter-antimatter molecules is a rather common phenomenon. We evaluate the binding energies and eigenstates of matter-antimatter molecules (μ + e - )-(e + μ - ),(π + e - )-(e + π - ),(K + e - )-(e + K - ),(pe - )-(e + p-bar),(pμ - )-(μ + p-bar), and (K + μ - ) - (μ + K - ), which satisfy the stability condition. We estimate the molecular annihilation lifetimes in their s states.

Quantifying small molecule phenotypic effects using mitochondrial morpho-functional fingerprinting and machine learning

Science.gov (United States)

Blanchet, Lionel; Smeitink, Jan A. M.; van Emst-de Vries, Sjenet E.; Vogels, Caroline; Pellegrini, Mina; Jonckheere, An I.; Rodenburg, Richard J. T.; Buydens, Lutgarde M. C.; Beyrath, Julien; Willems, Peter H. G. M.; Koopman, Werner J. H.

2015-01-01

In primary fibroblasts from Leigh Syndrome (LS) patients, isolated mitochondrial complex I deficiency is associated with increased reactive oxygen species levels and mitochondrial morpho-functional changes. Empirical evidence suggests these aberrations constitute linked therapeutic targets for small chemical molecules. However, the latter generally induce multiple subtle effects, meaning that in vitro potency analysis or single-parameter high-throughput cell screening are of limited use to identify these molecules. We combine automated image quantification and artificial intelligence to discriminate between primary fibroblasts of a healthy individual and a LS patient based upon their mitochondrial morpho-functional phenotype. We then evaluate the effects of newly developed Trolox variants in LS patient cells. This revealed that Trolox ornithylamide hydrochloride best counterbalanced mitochondrial morpho-functional aberrations, effectively scavenged ROS and increased the maximal activity of mitochondrial complexes I, IV and citrate synthase. Our results suggest that Trolox-derived antioxidants are promising candidates in therapy development for human mitochondrial disorders.

Modelling of energetic molecule-surface interactions

International Nuclear Information System (INIS)

Kerford, M.

2000-09-01

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

Possible reaction pathways of the lincomycin molecule according to the DFT calculation method

Directory of Open Access Journals (Sweden)

Eren Bahar

2017-01-01

Full Text Available Human-used antibiotics are eliminated from the body with little or no transformation at all. Traces of eliminated antibiotics enter the receiving environment directly since they cannot be treated in prevalent wastewater treatment facilities. Thus, wastewaters containing traces of antibiotics have to be treated accordingly. Lincomycin is subsequently isolated from Streptomyces lincolnensis. Lincomycin and its derivatives are antibiotics exhibiting biological activity against Gram-positive bacteria, and are natural antibiotics in the environment as pollutants. This study aims to predict the degradation mechanism of lincomycin molecule in the gaseous phase and aqueous media. Probable reaction path of lincomycin molecule with OH radicals was analyzed. Optimized geometry was calculated via Gauss View 5. Subsequently, the lowest energy status was determined through geometric optimization via Gaussian 09 program. Aiming to determine the intermediates in photocatalytic degradation mechanism of lincomycin, geometric optimization of the molecule was realized through DFT method. Activation energy for the probable reaction path was calculated, and their most stable state from the thermodynamic perspective determined for the gaseous phase and aqueous media. Impact of water solvent was investigated using the conductor-like screening solvation model (COSMO. The predicted mechanism was confirmed by comparison with experimental results on simple structures reported in literature.

Single-molecule dynamics in nanofabricated traps

Science.gov (United States)

Cohen, Adam

2009-03-01

The Anti-Brownian Electrokinetic trap (ABEL trap) provides a means to immobilize a single fluorescent molecule in solution, without surface attachment chemistry. The ABEL trap works by tracking the Brownian motion of a single molecule, and applying feedback electric fields to induce an electrokinetic motion that approximately cancels the Brownian motion. We present a new design for the ABEL trap that allows smaller molecules to be trapped and more information to be extracted from the dynamics of a single molecule than was previously possible. In particular, we present strategies for extracting dynamically fluctuating mobilities and diffusion coefficients, as a means to probe dynamic changes in molecular charge and shape. If one trapped molecule is good, many trapped molecules are better. An array of single molecules in solution, each immobilized without surface attachment chemistry, provides an ideal test-bed for single-molecule analyses of intramolecular dynamics and intermolecular interactions. We present a technology for creating such an array, using a fused silica plate with nanofabricated dimples and a removable cover for sealing single molecules within the dimples. With this device one can watch the shape fluctuations of single molecules of DNA or study cooperative interactions in weakly associating protein complexes.

Single molecules and nanotechnology

CERN Document Server

Vogel, Horst

2007-01-01

This book focuses on recent advances in the rapidly evolving field of single molecule research. These advances are of importance for the investigation of biopolymers and cellular biochemical reactions, and are essential to the development of quantitative biology. Written by leading experts in the field, the articles cover a broad range of topics, including: quantum photonics of organic dyes and inorganic nanoparticles their use in detecting properties of single molecules the monitoring of single molecule (enzymatic) reactions single protein (un)folding in nanometer-sized confined volumes the dynamics of molecular interactions in biological cells The book is written for advanced students and scientists who wish to survey the concepts, techniques and results of single molecule research and assess them for their own scientific activities.

A study on interaction of DNA molecules and carbon nanotubes for an effective ejection of the molecules

International Nuclear Information System (INIS)

Wu, N.; Wang, Q.

2012-01-01

The ejection of DNA molecules from carbon nanotubes is reported from interaction energy perspectives by molecular dynamics simulations. The critical ejection energy, which is to be applied to a DNA molecule for a successful ejection from a carbon nanotube, is investigated based on a study on the friction and binding energy between the DNA molecule and the tube. An effective ejection is realized by subjecting a kinetic energy on the DNA molecule that is larger than the solved critical ejection energy. In addition, the relationship between ejection energies and sizes of DNA molecules and carbon nanotubes is investigated. -- Highlights: ► Report the ejection of DNA molecules from CNTs from interaction energy perspectives. ► Develop a methodology for the critical energy of an effective ejection of a DNA molecule from a CNT. ► Present the relationship between critical ejection energies and sizes of DNA molecules and CNTs. ► Provide a general guidance on the ejection of encapsulated molecules from CNTs.

Organizing and addressing magnetic molecules.

Science.gov (United States)

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

2009-04-20

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

Lectin-Like Molecules of Lactobacillus rhamnosus GG Inhibit Pathogenic Escherichia coli and Salmonella Biofilm Formation.

Science.gov (United States)

Petrova, Mariya I; Imholz, Nicole C E; Verhoeven, Tine L A; Balzarini, Jan; Van Damme, Els J M; Schols, Dominique; Vanderleyden, Jos; Lebeer, Sarah

2016-01-01

Increased antibiotic resistance has catalyzed the research on new antibacterial molecules and alternative strategies, such as the application of beneficial bacteria. Since lectin molecules have unique sugar-recognizing capacities, and pathogens are often decorated with sugars that affect their survival and infectivity, we explored whether lectins from the probiotic strain Lactobacillus rhamnosus GG have antipathogenic properties. The genome sequence of L. rhamnosus GG was screened for the presence of lectin-like proteins. Two genes, LGG_RS02780 and LGG_RS02750, encoding for polypeptides with an N-terminal conserved L-type lectin domain were detected and designated Llp1 (lectin-like protein 1) and Llp2. The capacity of Llp1 and Llp2 to inhibit biofilm formation of various pathogens was investigated. Sugar specificity was determined by Sepharose beads assays and glycan array screening. The isolated lectin domains of Llp1 and Llp2 possess pronounced inhibitory activity against biofilm formation by various pathogens, including clinical Salmonella species and uropathogenic E. coli, with Llp2 being more active than Llp1. In addition, sugar binding assays with Llp1 and Llp2 indicate specificity for complex glycans. Both proteins are also involved in the adhesion capacity of L. rhamnosus GG to gastrointestinal and vaginal epithelial cells. Lectins isolated from or expressed by beneficial lactobacilli could be considered promising bio-active ingredients for improved prophylaxis of urogenital and gastrointestinal infections.

Observation of pendular butterfly Rydberg molecules

Science.gov (United States)

Niederprüm, Thomas; Thomas, Oliver; Eichert, Tanita; Lippe, Carsten; Pérez-Ríos, Jesús; Greene, Chris H.; Ott, Herwig

2016-01-01

Engineering molecules with a tunable bond length and defined quantum states lies at the heart of quantum chemistry. The unconventional binding mechanism of Rydberg molecules makes them a promising candidate to implement such tunable molecules. A very peculiar type of Rydberg molecules are the so-called butterfly molecules, which are bound by a shape resonance in the electron–perturber scattering. Here we report the observation of these exotic molecules and employ their exceptional properties to engineer their bond length, vibrational state, angular momentum and orientation in a small electric field. Combining the variable bond length with their giant dipole moment of several hundred Debye, we observe counter-intuitive molecules which locate the average electron position beyond the internuclear distance. PMID:27703143

Passing Current through Touching Molecules

DEFF Research Database (Denmark)

Schull, G.; Frederiksen, Thomas; Brandbyge, Mads

2009-01-01

The charge flow from a single C-60 molecule to another one has been probed. The conformation and electronic states of both molecules on the contacting electrodes have been characterized using a cryogenic scanning tunneling microscope. While the contact conductance of a single molecule between two...

Electron transport through a diatomic molecule

International Nuclear Information System (INIS)

Imran, Muhammad

2014-01-01

Electron transport through a diatomic molecular tunnel junction shows wave like interference phenomenon. By using Keldysh non-equilibrium Green's function (NEGF) theory, we have explicitly presented current and differential conductance calculation for a diatomic molecular and two isolated atoms (two atoms having zero hybridization between their energy orbitals) tunnel junctions. In case of a diatomic molecular tunnel junction, Green's function propagators entering into current and differential conductance formula interfere constructively for a molecular anti-bonding state and destructively for bonding state. Consequently, conductance through a molecular bonding state is suppressed, and to conserve current, conductance through anti-bonding state is enhanced. Therefore, current steps and differential conductance peaks amplitude show asymmetric correspondence between molecular bonding and anti-bonding states. Interestingly, for a diatomic molecule, comprising of two atoms of same energy level, these propagators interfere completely destructively for molecular bonding state and constructively for molecular anti-bonding state. Hence under such condition, a single step or a single peak is shown up in current versus voltage or differential conductance versus voltage studies.

Enzyme Molecules in Solitary Confinement

Directory of Open Access Journals (Sweden)

Raphaela B. Liebherr

2014-09-01

Full Text Available Large arrays of homogeneous microwells each defining a femtoliter volume are a versatile platform for monitoring the substrate turnover of many individual enzyme molecules in parallel. The high degree of parallelization enables the analysis of a statistically representative enzyme population. Enclosing individual enzyme molecules in microwells does not require any surface immobilization step and enables the kinetic investigation of enzymes free in solution. This review describes various microwell array formats and explores their applications for the detection and investigation of single enzyme molecules. The development of new fabrication techniques and sensitive detection methods drives the field of single molecule enzymology. Here, we introduce recent progress in single enzyme molecule analysis in microwell arrays and discuss the challenges and opportunities.

Complete genome sequences of two strains of the meat spoilage bacterium Brochothrix thermosphacta isolated from ground chicken

Science.gov (United States)

Brochothrix thermosphacta is an important meat spoilage bacterium. Here we report the genome sequences of two strains of B. thermosphacta isolated from ground chicken. The genome sequences were determined using long-read PacBio single-molecule real-time (SMRT©) technology and are the first complete ...

CD1 molecule expression on human monocytes induced by granulocyte-macrophage colony-stimulating factor.

Science.gov (United States)

Kasinrerk, W; Baumruker, T; Majdic, O; Knapp, W; Stockinger, H

1993-01-15

In this paper we demonstrate that granulocyte-macrophage CSF (GM-CSF) specifically induces the expression of CD1 molecules, CD1a, CD1b and CD1c, upon human monocytes. CD1 molecules appeared upon monocytes on day 1 of stimulation with rGM-CSF, and expression was up-regulated until day 3. Monocytes cultured in the presence of LPS, FMLP, PMA, recombinant granulocyte-CSF, rIFN-gamma, rTNF-alpha, rIL-1 alpha, rIL-1 beta, and rIL-6 remained negative. The induction of CD1 molecules by rGM-CSF was restricted to monocytes, since no such effect was observed upon peripheral blood granulocytes, PBL, and the myeloid cell lines Monomac1, Monomac6, MV4/11, HL60, U937, THP1, KG1, and KG1A. CD1a mRNA was detectable in rGM-CSF-induced monocytes but not in those freshly isolated. SDS-PAGE and immunoblotting analyses of CD1a mAb VIT6 immunoprecipitate from lysate of rGM-CSF-activated monocytes revealed an appropriate CD1a polypeptide band of 49 kDa associated with beta 2-microglobulin. Expression of CD1 molecules on monocytes complements the distribution of these structures on accessory cells, and their specific induction by GM-CSF strengthens the suggestion that CD1 is a family of crucial structures required for interaction between accessory cells and T cells.

A Mott-like State of Molecules

International Nuclear Information System (INIS)

Duerr, S.; Volz, T.; Syassen, N.; Bauer, D. M.; Hansis, E.; Rempe, G.

2006-01-01

We prepare a quantum state where each site of an optical lattice is occupied by exactly one molecule. This is the same quantum state as in a Mott insulator of molecules in the limit of negligible tunneling. Unlike previous Mott insulators, our system consists of molecules which can collide inelastically. In the absence of the optical lattice these collisions would lead to fast loss of the molecules from the sample. To prepare the state, we start from a Mott insulator of atomic 87Rb with a central region, where each lattice site is occupied by exactly two atoms. We then associate molecules using a Feshbach resonance. Remaining atoms can be removed using blast light. Our method does not rely on the molecule-molecule interaction properties and is therefore applicable to many systems

Quantum chaos and thermalization in isolated systems of interacting particles

Energy Technology Data Exchange (ETDEWEB)

Borgonovi, F., E-mail: fausto.borgonovi@unicatt.it [Dipartimento di Matematica e Fisica and Interdisciplinary Laboratories for Advanced Materials Physics, Universitá Cattolica, via Musei 41, 25121 Brescia, and INFN, Sezione di Pavia (Italy); Izrailev, F.M., E-mail: felix.izrailev@gmail.com [Instituto de Física, Universidad Autónoma de Puebla, Apt. Postal J-48, Puebla, Pue., 72570 (Mexico); NSCL and Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824-1321 (United States); Santos, L.F., E-mail: lsantos2@yu.edu [Department of Physics, Yeshiva University, 245 Lexington Ave, New York, NY 10016 (United States); Zelevinsky, V.G., E-mail: Zelevins@nscl.msu.edu [NSCL and Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824-1321 (United States)

2016-04-15

This review is devoted to the problem of thermalization in a small isolated conglomerate of interacting constituents. A variety of physically important systems of intensive current interest belong to this category: complex atoms, molecules (including biological molecules), nuclei, small devices of condensed matter and quantum optics on nano- and micro-scale, cold atoms in optical lattices, ion traps. Physical implementations of quantum computers, where there are many interacting qubits, also fall into this group. Statistical regularities come into play through inter-particle interactions, which have two fundamental components: mean field, that along with external conditions, forms the regular component of the dynamics, and residual interactions responsible for the complex structure of the actual stationary states. At sufficiently high level density, the stationary states become exceedingly complicated superpositions of simple quasiparticle excitations. At this stage, regularities typical of quantum chaos emerge and bring in signatures of thermalization. We describe all the stages and the results of the processes leading to thermalization, using analytical and massive numerical examples for realistic atomic, nuclear, and spin systems, as well as for models with random parameters. The structure of stationary states, strength functions of simple configurations, and concepts of entropy and temperature in application to isolated mesoscopic systems are discussed in detail. We conclude with a schematic discussion of the time evolution of such systems to equilibrium.

Towards efficient ab initio calculations of electron scattering by polyatomic molecules: III. Modelling correlation-polarization interactions

Czech Academy of Sciences Publication Activity Database

Čurík, Roman; Šulc, M.

2010-01-01

Roč. 43, č. 17 (2010), s. 175205 ISSN 0953-4075 R&D Projects: GA MŠk(CZ) OC10046; GA MŠk OC09079; GA AV ČR KJB400400803; GA ČR GA202/08/0631 Institutional research plan: CEZ:AV0Z40400503 Keywords : Ab initio calculations * Commonly used * DFT potential Subject RIV: CF - Physical ; The oretical Chemistry Impact factor: 1.902, year: 2010

Dissociation in small molecules

International Nuclear Information System (INIS)

Dehmer, P.M.

1982-01-01

The study of molecular dissociation processes is one of the most interesting areas of modern spectroscopy owing to the challenges presented bt even the simplest of diatomic molecules. This paper reviews the commonly used descriptions of molecular dissociation processes for diatomic molecules, the selection rules for predissociation, and a few of the principles to be remembered when one is forced to speculate about dissociation mechanisms in a new molecule. Some of these points will be illustrated by the example of dissociative ionization in O 2

A novel small molecule target in human airway smooth muscle for potential treatment of obstructive lung diseases: a staged high-throughput biophysical screening.

Science.gov (United States)

An, Steven S; Askovich, Peter S; Zarembinski, Thomas I; Ahn, Kwangmi; Peltier, John M; von Rechenberg, Moritz; Sahasrabudhe, Sudhir; Fredberg, Jeffrey J

2011-01-13

A newly identified mechanism of smooth muscle relaxation is the interaction between the small heat shock protein 20 (HSP20) and 14-3-3 proteins. Focusing upon this class of interactions, we describe here a novel drug target screening approach for treating airflow obstruction in asthma. Using a high-throughput fluorescence polarization (FP) assay, we screened a library of compounds that could act as small molecule modulators of HSP20 signals. We then applied two quantitative, cell-based biophysical methods to assess the functional efficacy of these molecules and rank-ordered their abilities to relax isolated human airway smooth muscle (ASM). Scaling up to the level of an intact tissue, we confirmed in a concentration-responsive manner the potency of the cell-based hit compounds. Among 58,019 compound tested, 268 compounds caused 20% or more reduction of the polarized emission in the FP assay. A small subset of these primary screen hits, belonging to two scaffolds, caused relaxation of isolated ASM cell in vitro and attenuated active force development of intact tissue ex vivo. This staged biophysical screening paradigm provides proof-of-principle for high-throughput and cost-effective discovery of new small molecule therapeutic agents for obstructive lung diseases.

A novel small molecule target in human airway smooth muscle for potential treatment of obstructive lung diseases: a staged high-throughput biophysical screening

Directory of Open Access Journals (Sweden)

von Rechenberg Moritz

2011-01-01

Full Text Available Abstract Background A newly identified mechanism of smooth muscle relaxation is the interaction between the small heat shock protein 20 (HSP20 and 14-3-3 proteins. Focusing upon this class of interactions, we describe here a novel drug target screening approach for treating airflow obstruction in asthma. Methods Using a high-throughput fluorescence polarization (FP assay, we screened a library of compounds that could act as small molecule modulators of HSP20 signals. We then applied two quantitative, cell-based biophysical methods to assess the functional efficacy of these molecules and rank-ordered their abilities to relax isolated human airway smooth muscle (ASM. Scaling up to the level of an intact tissue, we confirmed in a concentration-responsive manner the potency of the cell-based hit compounds. Results Among 58,019 compound tested, 268 compounds caused 20% or more reduction of the polarized emission in the FP assay. A small subset of these primary screen hits, belonging to two scaffolds, caused relaxation of isolated ASM cell in vitro and attenuated active force development of intact tissue ex vivo. Conclusions This staged biophysical screening paradigm provides proof-of-principle for high-throughput and cost-effective discovery of new small molecule therapeutic agents for obstructive lung diseases.

Cell Adhesion Molecules Are Mediated by Photobiomodulation at 660 nm in Diabetic Wounded Fibroblast Cells

Directory of Open Access Journals (Sweden)

Nicolette N. Houreld

2018-04-01

Full Text Available Diabetes affects extracellular matrix (ECM metabolism, contributing to delayed wound healing and lower limb amputation. Application of light (photobiomodulation, PBM has been shown to improve wound healing. This study aimed to evaluate the influence of PBM on cell adhesion molecules (CAMs in diabetic wound healing. Isolated human skin fibroblasts were grouped into a diabetic wounded model. A diode laser at 660 nm with a fluence of 5 J/cm2 was used for irradiation and cells were analysed 48 h post-irradiation. Controls consisted of sham-irradiated (0 J/cm2 cells. Real-time reverse transcription (RT quantitative polymerase chain reaction (qPCR was used to determine the expression of CAM-related genes. Ten genes were up-regulated in diabetic wounded cells, while 25 genes were down-regulated. Genes were related to transmembrane molecules, cell–cell adhesion, and cell–matrix adhesion, and also included genes related to other CAM molecules. PBM at 660 nm modulated gene expression of various CAMs contributing to the increased healing seen in clinical practice. There is a need for new therapies to improve diabetic wound healing. The application of PBM alongside other clinical therapies may be very beneficial in treatment.

Neutral molecules in tokamak edge plasma - role of vibrationally excited hydrogen molecules

International Nuclear Information System (INIS)

Cadez, I.; Cercek, M.; Pelicon, P.; Razpet, A.

2003-01-01

The role of neutral molecules in edge plasma is discussed with special emphasis on the vibrationally excited hydrogen. Neutral molecules are formed mostly by surface processes on the walls and then released to the edge plasma where they take part in volumetric reactions with other particles. Typically these molecules are formed in excited states and data are needed for their reactions on the wall and in the volume. Processes in edge plasma determine particle and energy flux what is especially critical issue in tokamak divertor region. Various cross sections and reaction rates are needed for modelling edge plasma and its interaction with walls. (author)

Single Molecule Analysis Research Tool (SMART: an integrated approach for analyzing single molecule data.

Directory of Open Access Journals (Sweden)

Max Greenfeld

Full Text Available Single molecule studies have expanded rapidly over the past decade and have the ability to provide an unprecedented level of understanding of biological systems. A common challenge upon introduction of novel, data-rich approaches is the management, processing, and analysis of the complex data sets that are generated. We provide a standardized approach for analyzing these data in the freely available software package SMART: Single Molecule Analysis Research Tool. SMART provides a format for organizing and easily accessing single molecule data, a general hidden Markov modeling algorithm for fitting an array of possible models specified by the user, a standardized data structure and graphical user interfaces to streamline the analysis and visualization of data. This approach guides experimental design, facilitating acquisition of the maximal information from single molecule experiments. SMART also provides a standardized format to allow dissemination of single molecule data and transparency in the analysis of reported data.

Polarization effects on the electric properties of urea and thiourea molecules in solid phase

International Nuclear Information System (INIS)

Santos, O. L.; Fonseca, T. L.; Sabino, J. R.; Georg, H. C.; Castro, M. A.

2015-01-01

We present theoretical results for the dipole moment, linear polarizability, and first hyperpolarizability of the urea and thiourea molecules in solid phase. The in-crystal electric properties were determined by applying a supermolecule approach in combination with an iterative electrostatic scheme, in which the surrounding molecules are represented by point charges. It is found for both urea and thiourea molecules that the influence of the polarization effects is mild for the linear polarizability, but it is marked for the dipole moment and first hyperpolarizability. The replacement of oxygen atoms by sulfur atoms increases, in general, the electric responses. Our second-order Møller–Plesset perturbation theory based iterative scheme predicts for the in-crystal dipole moment of urea and thiourea the values of 7.54 and 9.19 D which are, respectively, increased by 61% and 58%, in comparison with the corresponding isolated values. The result for urea is in agreement with the available experimental result of 6.56 D. In addition, we present an estimate of macroscopic quantities considering explicit unit cells of urea and thiourea crystals including environment polarization effects. These supermolecule calculations take into account partially the exchange and dispersion effects. The results illustrate the role played by the electrostatic interactions on the static second-order nonlinear susceptibility of the urea crystal

Phase-locked high-order-harmonic and sub-100-as pulse generation from stretched molecules

International Nuclear Information System (INIS)

Lan Pengfei; Lu Peixiang; Cao Wei; Wang Xinlin; Yang Guang

2006-01-01

High harmonic generation from diatomic molecules in a linearly polarized intense laser field is investigated and the emission time of the harmonics is discussed with the time-frequency analysis method. It is shown that high harmonic generation from molecules at equilibrium distance is similar to that from atoms. Only the harmonics in the cutoff are synchronized, i.e., well phase-locked, whereas the other harmonics are not phase-locked. For the molecule stretched well beyond its equilibrium distance, the harmonics exhibit distinct time-frequency characteristics. The harmonic spectrum can be extended to I p +8U p , where I p and U p are the ionization and ponderomotive potential, and the harmonics with energies below I p +3.17U p are not phase-locked and the harmonics with energies beyond I p +3.17U p are well phase-locked. Thus a large range of harmonics which are well phase-locked are produced, and a train of clean attosecond (as) pulses with a single 90-as pulse in each half optical cycle can be generated with a multicycle laser pulse. Using a few-cycle laser pulse, an isolated attosecond pulse with a duration of about 95 as is obtained

Exotic helium molecules

International Nuclear Information System (INIS)

Portier, M.

2007-12-01

We study the photo-association of an ultracold cloud of magnetically trapped helium atoms: pairs of colliding atoms interact with one or two laser fields to produce a purely long range 4 He 2 (2 3 S 1 -2 3 P 0 ) molecule, or a 4 He 2 (2 3 S 1 -2 3 S 1 ) long range molecule. Light shifts in one photon photo-association spectra are measured and studied as a function of the laser polarization and intensity, and the vibrational state of the excited molecule. They result from the light-induced coupling between the excited molecule, and bound and scattering states of the interaction between two metastable atoms. Their analysis leads to the determination of the scattering length a = (7.2 ± 0.6) ruling collisions between spin polarized atoms. The two photon photo-association spectra show evidence of the production of polarized, long-range 4 He 2 (2 3 S 1 -2 3 S 1 ) molecules. They are said to be exotic as they are made of two metastable atoms, each one carrying a enough energy to ionize the other. The corresponding lineshapes are calculated and decomposed in sums and products of Breit-Wigner and Fano profiles associated to one and two photon processes. The experimental spectra are fit, and an intrinsic lifetime τ = (1.4 ± 0.3) μs is deduced. It is checked whether this lifetime could be limited by spin-dipole induced Penning autoionization. This interpretation requires that there is a quasi-bound state close to the dissociation threshold in the singlet interaction potential between metastable helium atoms for the theory to match the experiment. (author)

Cold guided beams of polar molecules

International Nuclear Information System (INIS)

Motsch, Michael

2010-01-01

This thesis reports on experiments characterizing cold guided beams of polar molecules which are produced by electrostatic velocity filtering. This filtering method exploits the interaction between the polar molecules and the electric field provided by an electrostatic quadrupole guide to extract efficiently the slow molecules from a thermal reservoir. For molecules with large and linear Stark shifts such as deuterated ammonia (ND 3 ) or formaldehyde (H 2 CO), fluxes of guided molecules of 10 10 -10 11 molecules/s are produced. The velocities of the molecules in these beams are in the range of 10-200 m/s and correspond to typical translational temperatures of a few Kelvin. The maximum velocity of the guided molecules depends on the Stark shift, the molecular mass, the geometry of the guide, and the applied electrode voltage. Although the source is operated in the near-effusive regime, the number density of the slowest molecules is sensitive to collisions. A theoretical model, taking into account this velocity-dependent collisional loss of molecules in the vicinity of the nozzle, reproduces the density of the guided molecules over a wide pressure range. A careful adjustment of pressure allows an increase in the total number of molecules, whilst yet minimizing losses due to collisions of the sought-for slow molecules. This is an important issue for future applications. Electrostatic velocity filtering is suited for different molecular species. This is demonstrated by producing cold guided beams of the water isotopologs H 2 O, D 2 O, and HDO. Although these are chemically similar, they show linear and quadratic Stark shifts, respectively, when exposed to external electric fields. As a result, the flux of HDO is larger by one order of magnitude, and the flux of the individual isotopologs shows a characteristic dependence on the guiding electric field. The internal-state distribution of guided molecules is studied with a newly developed diagnostic method: depletion

Oxides with polyatomic anions considered as new electrolyte materials for solid oxide fuel cells (SOFCs)

Energy Technology Data Exchange (ETDEWEB)

Bin Hassan, Oskar Hasdinor

2010-10-21

Materials with Polyatomic anions of [Al{sub 2}O{sub 7}]{sup -8}, [Ti{sub 2}O{sub 8}]{sup -8} and [P{sub 2}O{sub 7}]{sup -4} were investigated with respect to their ionic conductivity properties as well as its thermal expansion properties with the aim to use them as SOFCs electrolytes. The polyatomic anion groups selected from the oxy-cuspidine family of Gd{sub 4}Al{sub 2}O{sub 9} and Gd{sub 4}Ti{sub 2}O{sub 10} as well as from pyrophosphate SnP{sub 2}O{sub 7}. The pure oxy-cuspidine Gd{sub 4}Al{sub 2}O{sub 9}, the series of Gd{sub 4}Al{sub 2-x}Mg{sub x}O{sub 9-x/2} with x=0.10-1.0 and Gd{sub 4-x}M{sub x}Al{sub 2}O{sub 9-x/2} (M=Ca, Sr) with x = 0.05-0.5 were prepared successfully by the citrate complexation method. All samples showed the crystal structure of monoclinic oxycuspidine structure with space group of P2{sub 1/c} and Z=4. No solid solution was observed for Gd{sub 4}Al{sub 2-x}Mg{sub x}O{sub 9-x/2} where additional phases of Gd{sub 2}O{sub 3} and MgO were presence. XRD semiquantitative analysis together with SEM-EDX analysis revealed that Mg{sup 2+} was not able to substitute the Al{sup 3+} ions even at low Mg{sup 2+} concentration. The solid solution limit of Gd{sub 4-x}Ca{sub x}Al{sub 2}O{sub 9-x/2} and Gd{sub 4-x}Sr{sub x}Al{sub 2}O{sub 9-x/2} was determined between 0.05-0.10 and 0.01-0.05 mol for Ca and Sr, respectively. Beyond the substitution limit Gd{sub 4}Al{sub 2}O{sub 9}, GdAlO{sub 3} and SrGd{sub 2}Al{sub 2}O{sub 7} appeared as additional phases. The highest electrical conductivity obtained at 900 C yielded {sigma}= 1.49 x 10{sup -4}Scm{sup -1} for Gd{sub 3.95}Ca{sub 0.05}Al{sub 2}O{sub 8.98}. In comparison, the conductivity of pure Gd{sub 4}Al{sub 2}O{sub 9} was {sigma}= 1.73 x 10{sup -5} Scm{sup -1}. The conductivities determined were in a similar range as those of other cuspidine materials investigated previously. The thermal expansion coefficient of Gd{sub 4}Al{sub 2}O{sub 9} at 1000 C was 7.4 x 10{sup -6}K{sup -1}. The earlier reported

The effect of lidocaine on in vitro neutrophil and endothelial adhesion molecule expression induced by plasma obtained during tourniquet-induced ischaemia and reperfusion.

LENUS (Irish Health Repository)

Lan, W

2012-02-03

BACKGROUND: Changes in neutrophil and endothelial adhesion molecule expression occur during perioperative ischaemia and reperfusion (I\\/R) injury. We investigated the effects of lidocaine on neutrophil-independent changes in neutrophil and endothelial adhesion molecule expression associated with tourniquet-induced I\\/R. METHODS: Plasma was obtained from venous blood samples (tourniquet arm) taken before (baseline), during, 15 min, 2 and 24 h following tourniquet release in seven patients undergoing elective upper limb surgery with tourniquet application. Isolated neutrophils from healthy volunteers (n = 7) were pretreated in the presence or absence of lidocaine (0.005, 0.05 and 0.5 mg mL(-1) for 1 h, and then incubated with I\\/R plasma for 2 h. Human umbilical vein endothelial cells (HUVECs) were pretreated in the presence or absence of lidocaine (0.005, 0.05 and 0.5 mg mL(-1)) for 1 h, and then incubated with the plasma for 4 h. Adhesion molecule expression was estimated using flow cytometry. Data were analysed using ANOVA and post hoc Student-Newman-Keuls tests. RESULTS: I\\/R plasma (withdrawn 15 min following tourniquet release) increased isolated neutrophil CD11b (P = 0.03), CD18 (P = 0.01) and endothelial intercellular adhesion molecule-1 (ICAM-1) (P = 0.008) expression compared to baseline. CD11b, CD18 and ICAM-1 expression on lidocaine (0.005 mg mL(-1)) treated neutrophils was similar to control. CD11b (P < 0.001), CD18 (P = 0.03) and ICAM-1 (P = 0.002) expression on lidocaine (0.05 mg mL(-1)) treated neutrophils and HUVECs was less than that on controls. CONCLUSION: Increased in vitro neutrophil and endothelial cell adhesion molecule expression on exposure to plasma obtained during the early reperfusion phase is diminished by lidocaine at greater than clinically relevant plasma concentrations.

Molecule of the Month

Indian Academy of Sciences (India)

Atoms in a molecule generally prefer, particularly among the neighbouring ones, certain optimmn geometrical relationships. These are manifested in specific ranges of bond lengths, bond angles, torsion angles etc. As it always happens, chemists are interested in making molecules where these 'standard relationships' are ...

Sesquiterpene lactones isolated from indigenous Middle Eastern plants inhibit tumor promoter-induced transformation of JB6 cells

Directory of Open Access Journals (Sweden)

Saikali Melody

2012-07-01

Full Text Available Abstract Background Sesquiterpene lactones (SL are plant secondary metabolites that are known for their anti-fungal, anti-bacterial, anti-inflammatory, and anti-tumor properties. Considering that several SL-derived drugs are currently in cancer clinical trials, we have tested two SL molecules, 3-β-methoxy-iso-seco-tanapartholide (β-tan isolated from Achillea falcata and salograviolide A (Sal A isolated from Centaurea ainetensis, for their anti-tumor properties. We used the mouse epidermal JB6P + cells as a model for tumor promotion and cellular transformation. Key players that are involved in cellular transformation and tumorigenesis are the AP-1 and NF-κB transcription factors; therefore, we assessed how β-tan and Sal A modulate their signaling pathways in JB6P + cells. Methods The effects of β-tan and Sal A on the growth of normal and neoplastic keratinocytes and on the tumor promotion-responsive JB6P + cells were determined using the MTT assay. Anchorage-independent cell growth transformation assays were used to evaluate the anti-tumor promoting properties of these SL molecules in JB6P + cells and dual luciferase reporter assays and western blot analysis were used to investigate their effects on tumor promoter-induced AP-1 and NF-κB activities and protein levels of key AP-1 and NF-кB target genes. Results β-tan and Sal A selectively inhibited tumor promoter-induced cell growth and transformation of JB6P + cells at concentrations that do not affect JB6P + and primary keratinocytes basal cell growth. In addition, both molecules reduced basal and tumor promoter-induced NF-κB transcriptional activities, differentially regulated basal and tumor promoter-induced AP-1 transcriptional activities, and modulated key players of the AP-1 and NF-κB signaling pathways. Conclusions These results highlight the anti-tumor promoting properties of β-tan and Sal A. These SL molecules isolated from two plant species native to

Sesquiterpene lactones isolated from indigenous Middle Eastern plants inhibit tumor promoter-induced transformation of JB6 cells.

Science.gov (United States)

Saikali, Melody; Ghantous, Akram; Halawi, Racha; Talhouk, Salma N; Saliba, Najat A; Darwiche, Nadine

2012-07-09

Sesquiterpene lactones (SL) are plant secondary metabolites that are known for their anti-fungal, anti-bacterial, anti-inflammatory, and anti-tumor properties. Considering that several SL-derived drugs are currently in cancer clinical trials, we have tested two SL molecules, 3-β-methoxy-iso-seco-tanapartholide (β-tan) isolated from Achillea falcata and salograviolide A (Sal A) isolated from Centaurea ainetensis, for their anti-tumor properties. We used the mouse epidermal JB6P + cells as a model for tumor promotion and cellular transformation. Key players that are involved in cellular transformation and tumorigenesis are the AP-1 and NF-κB transcription factors; therefore, we assessed how β-tan and Sal A modulate their signaling pathways in JB6P + cells. The effects of β-tan and Sal A on the growth of normal and neoplastic keratinocytes and on the tumor promotion-responsive JB6P + cells were determined using the MTT assay. Anchorage-independent cell growth transformation assays were used to evaluate the anti-tumor promoting properties of these SL molecules in JB6P + cells and dual luciferase reporter assays and western blot analysis were used to investigate their effects on tumor promoter-induced AP-1 and NF-κB activities and protein levels of key AP-1 and NF-кB target genes. β-tan and Sal A selectively inhibited tumor promoter-induced cell growth and transformation of JB6P + cells at concentrations that do not affect JB6P + and primary keratinocytes basal cell growth. In addition, both molecules reduced basal and tumor promoter-induced NF-κB transcriptional activities, differentially regulated basal and tumor promoter-induced AP-1 transcriptional activities, and modulated key players of the AP-1 and NF-κB signaling pathways. These results highlight the anti-tumor promoting properties of β-tan and Sal A. These SL molecules isolated from two plant species native to the Middle East may provide opportunities for complementary

Isolation of homoleptic platinum oxyanionic complexes with doubly protonated diazacrown cation

Science.gov (United States)

Vasilchenko, Danila; Tkachev, Sergey; Baidina, Iraida; Romanenko, Galina; Korenev, Sergey

2017-02-01

Doubly protonated diazacrown ether cation (1,4,10,13-tetraoxa-7,16-diazoniacyclooctadecane DCH22+) was used for the efficient isolation of the homoleptic platinum complexes [Pt(NO3)6]2- and [Pt(C2O4)2]2- to crystalline solid phases from solutions containing mixtures of related platinum complexes. DCH22+ molecules in nitric acid solution were shown to prevent the condensation of mononuclear [Pt(H2O)n(NO3)6-n]n-2 species.

Dissociation and decay of ultracold sodium molecules

International Nuclear Information System (INIS)

Mukaiyama, T.; Abo-Shaeer, J.R.; Xu, K.; Chin, J.K.; Ketterle, W.

2004-01-01

The dissociation of ultracold molecules was studied by ramping an external magnetic field through a Feshbach resonance. The observed dissociation energies directly yielded the strength of the atom-molecule coupling. They showed nonlinear dependence on the ramp speed. This was explained by a Wigner threshold law which predicts that the decay rate of the molecules above threshold increases with the density of states. In addition, inelastic molecule-molecule and molecule-atom collisions were characterized

Single-Molecule Interfacial Electron Transfer

Energy Technology Data Exchange (ETDEWEB)

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

2017-11-28

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

Isolation and characterization of biosurfactant producing bacteria from Persian Gulf (Bushehr provenance).

Science.gov (United States)

Hassanshahian, Mehdi

2014-09-15

Biosurfactants are surface active materials that are produced by some microorganisms. These molecules increase biodegradation of insoluble pollutants. In this study sediments and seawater samples were collected from the coastline of Bushehr provenance in the Persian Gulf and their biosurfactant producing bacteria were isolated. Biosurfactant producing bacteria were isolated by using an enrichment method in Bushnell-Hass medium with diesel oil as the sole carbon source. Five screening tests were used for selection of Biosurfactant producing bacteria: hemolysis in blood agar, oil spreading, drop collapse, emulsification activity and Bacterial Adhesion to Hydrocarbon test (BATH). These bacteria were identified using biochemical and molecular methods. Eighty different colonies were isolated from the collected samples. The most biosurfactant producing isolates related to petrochemical plants of Khark Island. Fourteen biosurfactant producing bacteria were selected between these isolates and 7 isolates were screened as these were predominant producers that belong to Shewanella alga, Shewanella upenei, Vibrio furnissii, Gallaecimonas pentaromativorans, Brevibacterium epidermidis, Psychrobacter namhaensis and Pseudomonas fluorescens. The largest clear zone diameters in oil spreading were observed for G. pentaromativorans strain O15. Also, this strain has the best emulsification activity and reduction of surface tension, suggesting it is the best of thee isolated strains. The results of this study confirmed that there is high diversity of biosurfactant producing bacteria in marine ecosystem of Iran and by application of these bacteria in petrochemical waste water environmental problems can be assisted. Copyright © 2014 Elsevier Ltd. All rights reserved.

Enrichment of megabase-sized DNA molecules for single-molecule optical mapping and next-generation sequencing

DEFF Research Database (Denmark)

Łopacińska-Jørgensen, Joanna M; Pedersen, Jonas Nyvold; Bak, Mads

2017-01-01

Next-generation sequencing (NGS) has caused a revolution, yet left a gap: long-range genetic information from native, non-amplified DNA fragments is unavailable. It might be obtained by optical mapping of megabase-sized DNA molecules. Frequently only a specific genomic region is of interest, so......-megabase- to megabase-sized DNA molecules were recovered from the gel and analysed by denaturation-renaturation optical mapping. Size-selected molecules from the same gel were sequenced by NGS. The optically mapped molecules and the NGS reads showed enrichment from regions defined by NotI restriction sites. We...... demonstrate that the unannotated genome can be characterized in a locus-specific manner via molecules partially overlapping with the annotated genome. The method is a promising tool for investigation of structural variants in enriched human genomic regions for both research and diagnostic purposes. Our...

Theory of attosecond delays in molecular photoionization.

Science.gov (United States)

Baykusheva, Denitsa; Wörner, Hans Jakob

2017-03-28

We present a theoretical formalism for the calculation of attosecond delays in molecular photoionization. It is shown how delays relevant to one-photon-ionization, also known as Eisenbud-Wigner-Smith delays, can be obtained from the complex dipole matrix elements provided by molecular quantum scattering theory. These results are used to derive formulae for the delays measured by two-photon attosecond interferometry based on an attosecond pulse train and a dressing femtosecond infrared pulse. These effective delays are first expressed in the molecular frame where maximal information about the molecular photoionization dynamics is available. The effects of averaging over the emission direction of the electron and the molecular orientation are introduced analytically. We illustrate this general formalism for the case of two polyatomic molecules. N 2 O serves as an example of a polar linear molecule characterized by complex photoionization dynamics resulting from the presence of molecular shape resonances. H 2 O illustrates the case of a non-linear molecule with comparably simple photoionization dynamics resulting from a flat continuum. Our theory establishes the foundation for interpreting measurements of the photoionization dynamics of all molecules by attosecond metrology.

Preface: Special Topic on Single-Molecule Biophysics.

Science.gov (United States)

Makarov, Dmitrii E; Schuler, Benjamin

2018-03-28

Single-molecule measurements are now almost routinely used to study biological systems and processes. The scope of this special topic emphasizes the physics side of single-molecule observations, with the goal of highlighting new developments in physical techniques as well as conceptual insights that single-molecule measurements bring to biophysics. This issue also comprises recent advances in theoretical physical models of single-molecule phenomena, interpretation of single-molecule signals, and fundamental areas of statistical mechanics that are related to single-molecule observations. A particular goal is to illustrate the increasing synergy between theory, simulation, and experiment in single-molecule biophysics.

The role of the ion-molecule and molecule-molecule interactions in the formation of the two-ion average force interaction potential

CERN Document Server

Ajrian, E A; Sidorenko, S N

2002-01-01

The effect of the ion-molecule and intermolecular interactions on the formation of inter-ion average force potentials is investigated within the framework of a classical ion-dipole model of electrolyte solutions. These potentials are shown to possess the Coulomb asymptotics at large distances while in the region of mean distances they reveal creation and disintegration of solvent-shared ion pairs. The calculation results provide a qualitatively authentic physical picture which is experimentally observed in strong electrolytes solutions. In particular, an increased interaction between an ion and a molecule enhances formation of ion pairs in which the ions are separated by one solvent molecule

Tandem Mass Spectrometry Detection of Quorum Sensing Activity in Multidrug Resistant Clinical Isolate Acinetobacter baumannii

Directory of Open Access Journals (Sweden)

Kok-Gan Chan

2014-01-01

Full Text Available Many Proteobacteria communicate via production followed by response of quorum sensing molecules, namely, N-acyl homoserine lactones (AHLs. These molecules consist of a lactone moiety with N-acyl side chain with various chain lengths and degrees of saturation at C-3 position. AHL-dependent QS is often associated with regulation of diverse bacterial phenotypes including the expression of virulence factors. With the use of biosensor and high resolution liquid chromatography tandem mass spectrometry, the AHL production of clinical isolate A. baumannii 4KT was studied. Production of short chain AHL, namely, N-hexanoyl-homoserine lactone (C6-HSL and N-octanoyl-homoserine lactone (C8-HSL, was detected.

Labelled molecules, modern research implements

International Nuclear Information System (INIS)

Pichat, L.; Langourieux, Y.

1974-01-01

Details of the synthesis of carbon 14- and tritium-labelled molecules are examined. Although the methods used are those of classical organic chemistry the preparation of carbon 14-labelled molecules differs in some respects, most noticeably in the use of 14 CO 2 which requires very special handling techniques. For the tritium labelling of organic molecules the methods are somewhat different, very often involving exchange reactions. The following are described in turn: the so-called Wilzbach exchange method; exchange by catalysis in solution; catalytic hydrogenation with tritium; reductions with borotritides. Some applications of labelled molecules in organic chemistry, biochemistry and pharmacology are listed [fr

Hybrid molecule/superconductor assemblies

International Nuclear Information System (INIS)

McDevitt, J.T.; Haupt, S.G.; Riley, D.R.; Zhao, J.; Zhou, J.P., Jones, C.

1993-01-01

The fabrication of electronic devices from molecular materials has attracted much attention recently. Schottky diodes, molecular transistors, metal-insulator-semiconductor diodes, MIS field effect transistors and light emitting diodes have all been prepared utilizing such substances. The active elements in these devices have been constructed by depositing the molecular phase onto the surface of a metal, semiconductor or insulating substrate. With the recent discovery of high temperature superconductivity, new opportunities now exist for the study of molecule/superconductor interactions as well as for the construction of novel hybrid molecule/superconductor devices. In this paper, methods for preparing the initial two composite molecule/semiconductor devices will be reported. Consequently, light sensors based on dye-coated superconductor junctions as well as molecular switches fashioned from conductive polymer coated superconductor junctions as well as molecular switches fashioned from conductive polymer coated superconductor microbridges will be discussed. Moreover, molecule/superconductor energy and electron transfer phenomena will be illustrated also for the first time

Role of electronic correlations in photoionization of NO2 in the vicinity of the 2A1/2B2 conical intersection.

Science.gov (United States)

Brambila, Danilo S; Harvey, Alex G; Houfek, Karel; Mašín, Zdeněk; Smirnova, Olga

2017-08-02

We present the first ab initio multi-channel photoionization calculations for NO 2 in the vicinity of the 2 A 1 / 2 B 2 conical intersection, for a range of nuclear geometries, using our newly developed set of tools based on the ab initio multichannel R-matrix method. Electronic correlation is included in both the neutral and the scattering states of the molecule via configuration interaction. Configuration mixing is especially important around conical intersections and avoided crossings, both pertinent for NO 2 , and manifests itself via significant variations in photoelectron angular distributions. The method allows for a balanced and accurate description of the photoionization/photorecombination for a number of different ionic channels in a wide range of photoelectron energies up to 100 eV. Proper account of electron correlations is crucial for interpreting time-resolved signals in photoelectron spectroscopy and high harmonic generation (HHG) from polyatomic molecules.

Quantitative degenerate four-wave mixing spectroscopy: Probes for molecular species

Energy Technology Data Exchange (ETDEWEB)

Farrow, R.; Rakestraw, D.; Paul, P.; Lucht, R.; Danehy, P.; Friedman-Hill, E.; Germann, G. [Sandia National Laboratories, Livermore, CA (United States)

1993-12-01

Resonant degenerate four-wave mixing (DFWM) is currently the subject of intensive investigation as a sensitive diagnostic tool for molecular species. DFWM has the advantage of generating a coherent (beam-like) signal which results in null-background detection and provides excellent immunity to background-light interference. Since multiple one-photon resonances are involved in the signal generation process, the DFWM technique can allow sensitive detection of molecules via electronic, vibrational or rotational transitions. These properties combine to make DFWM a widely applicable diagnostic technique for the probing of molecular species. The authors are conducting fundamental and applied investigations of DFWM for quantitative measurements of trace species in reacting gases. During the past year, efforts have been focussed in two areas: (1) understanding the effects of collisional processes on the DFWM signal generation process, and (2) exploring the applicability of infrared DFWM to detect polyatomic molecules via rovibrational transitions.

Photo-electron spectroscopy using synchrotron radiation of molecular radicals and fragments produced by laser photo-dissociation

International Nuclear Information System (INIS)

Nahon, Laurent

1991-01-01

This research thesis reports the combined use of a laser and of a synchrotron radiation in order to respectively photo-dissociate a molecule and to photo-ionize fragments which are analysed by photo-electron spectroscopy. This association allows, on the one hand, radical photo-ionization to be studied, and, on the other hand, polyatomic molecule photo-dissociation to be studied. The author studied the photo-excitation and/or photo-ionization in layer 4d (resp. 3d) of atomic iodine (resp. bromine) produced almost complete laser photo-dissociation of I_2 (resp. Br_2). He discuses the processes of relaxation of transitions from valence 4d to 5p (resp. 3d to 4p) which occur either by direct self-ionization or by resonant Auger effect, and reports the study of photo-dissociation of s-tetrazine (C_2N_4H_2) [fr

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

DEFF Research Database (Denmark)

Zhang, Jingdong; Chi, Qijin; Ulstrup, Jens

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

Sputtering of thin benzene and polystyrene overlayers by keV Ga and C60 bombardment

International Nuclear Information System (INIS)

Czerwinski, B.; Delcorte, A.; Garrison, B.J.; Samson, R.; Winograd, N.; Postawa, Z.

2006-01-01

The mechanisms of ion-stimulated desorption of thin organic overlayers deposited on metal substrates by mono- and polyatomic projectiles are examined using molecular dynamics (MD) computer simulations. A monolayer of polystyrene tetramers (PS4) physisorbed on Ag{1 1 1} is irradiated by 15 keV Ga and C 60 projectiles at normal incidence. The results are compared with the data obtained for a benzene overlayer to investigate the differences in sputtering mechanisms of weakly and strongly bound organic molecules. The results indicate that the sputtering yield decreases with the increase of the binding energy and the average kinetic energy of parent molecules is shifted toward higher kinetic energy. Although the total sputtering yield of organic material is larger for 15 keV C 60 , the impact of this projectile leads to a significant fragmentation of ejected species. As a result, the yield of the intact molecules is comparable for C 60 and Ga projectiles. Our data indicate that chemical analysis of the very thin organic films performed by detection of sputtered neutrals will not benefit from the use of C 60 projectiles

Isolation and partial characterization of Brazilian samples of feline immunodeficiency virus.

Science.gov (United States)

Teixeira, B M; Logan, N; Samman, A; Miyashiro, S I; Brandão, P E; Willett, B J; Hosie, M J; Hagiwara, M K

2011-09-01

Feline immunodeficiency virus (FIV) causes a slow progressive degeneration of the immune system which eventually leads to a disease comparable to acquired immune deficiency syndrome (AIDS) in humans. FIV has extensive sequence variation, a typical feature of lentiviruses. Sequence analysis showed that diversity was not evenly distributed throughout the genome, but was greatest in the envelope gene, env. The virus enters host cells via a sequential interaction, initiated by the envelope glycoprotein (env) binding the primary receptor molecule CD134 and followed by a subsequent interaction with chemokine co-receptor CXCR4. The purpose of this study was to isolate and characterize isolates of FIV from an open shelter in São Paulo, Brazil. The separated PBMC from 11 positive cats were co-cultured with MYA-1 cells. Full-length viral env glycoprotein genes were amplified and determined. Chimeric feline × human CD134 receptors were used to investigate the receptor utilization of 17 clones from Brazilian isolates of FIV. Analyses of the sequence present of molecular clones showed that all clones grouped within subtype B. In contrast to the virulent primary isolate FIV-GL8, expression of the first cysteine-rich domain (CRD1) of feline CD134 in the context of human CD134 was sufficient for optimal receptor function for all Brazilian FIV isolates tested. Copyright © 2011 Elsevier B.V. All rights reserved.

Isolation of antigenic substances from HIV-1 envelope gp160 gene transfectants by mild acid elution and X-irradiation treatment. For the development of CTL-based immunotherapy

International Nuclear Information System (INIS)

Fujimoto, Chiaki; Nakagawa, Yohko; Shimizu, Masumi; Ohara, Kunitoshi; Takahashi, Hidemi

2003-01-01

Cytotoxic T lymphocytes (CTLs) play a central role in a broad spectrum of tumor immunity. Such CTLs generally recognize processed antigenic fragments in association with class I major histocompatibility complex (MHC) molecules. Thus, it is important to identify naturally processed antigens associated with class I MHC molecules to generate and activate antigen-specific CTLs. Those processed antigens fitted in the groove of class I MHC molecules are fixed by the β2-microglobulin. Mild acid elution is one method used to isolate antigenic fragments from class I MHC molecules on tumor cells by unfastening a clasp of β2-microglobulin, a critical component for stabilizing class I MHC molecules on the cell surface. Indeed, after the mild acid treatment, the expression of class I MHC molecules was temporarily down-modulated and a strong antigenic fraction for CTL recognition was obtained. To our surprise, such down-modulation of class I MHC molecule expression was also observed when the tumor cells were irradiated. Therefore, using human immunodeficiency virus type I (HIV-1) gp160 env gene transfectants, we examined the effect of X-irradiation on releasing the loaded antigenic fragments. Functional extracts were obtained from X-irradiated cell supernatants that sensitized syngeneic fibroblasts for specific CTL recognition, suggesting that X-irradiation extracts would also contain known antigenic epitopes. These results indicate that, in addition to the conventional mild acid elution treatment, X-irradiation method shown in this paper may provide a new approach for CTL-based vaccine development via isolating antigenic molecules from various tumors or virally infected cells. (author)

Lectin-Like Molecules of Lactobacillus rhamnosus GG Inhibit Pathogenic Escherichia coli and Salmonella Biofilm Formation

Science.gov (United States)

Petrova, Mariya I.; Imholz, Nicole C. E.; Verhoeven, Tine L. A.; Balzarini, Jan; Van Damme, Els J. M.; Schols, Dominique; Vanderleyden, Jos; Lebeer, Sarah

2016-01-01

Objectives Increased antibiotic resistance has catalyzed the research on new antibacterial molecules and alternative strategies, such as the application of beneficial bacteria. Since lectin molecules have unique sugar-recognizing capacities, and pathogens are often decorated with sugars that affect their survival and infectivity, we explored whether lectins from the probiotic strain Lactobacillus rhamnosus GG have antipathogenic properties. Methods The genome sequence of L. rhamnosus GG was screened for the presence of lectin-like proteins. Two genes, LGG_RS02780 and LGG_RS02750, encoding for polypeptides with an N-terminal conserved L-type lectin domain were detected and designated Llp1 (lectin-like protein 1) and Llp2. The capacity of Llp1 and Llp2 to inhibit biofilm formation of various pathogens was investigated. Sugar specificity was determined by Sepharose beads assays and glycan array screening. Results The isolated lectin domains of Llp1 and Llp2 possess pronounced inhibitory activity against biofilm formation by various pathogens, including clinical Salmonella species and uropathogenic E. coli, with Llp2 being more active than Llp1. In addition, sugar binding assays with Llp1 and Llp2 indicate specificity for complex glycans. Both proteins are also involved in the adhesion capacity of L. rhamnosus GG to gastrointestinal and vaginal epithelial cells. Conclusions Lectins isolated from or expressed by beneficial lactobacilli could be considered promising bio-active ingredients for improved prophylaxis of urogenital and gastrointestinal infections. PMID:27537843

Isolation and crystal structure determination of piperazine dicarbamate obtained from a direct reaction

Energy Technology Data Exchange (ETDEWEB)

Sim, Jae Ung; Jo, Eun Hee; Jhon, Young Ho; Paek, Kyung Soo; Kim, Ja Heon [Dept. of Chemistry, Soongsil University, Seoul (Korea, Republic of); Jang Se Gyu; Shim, Jae Goo; Jang, Kyung Ryong [Korea Future Technology Research Laboratory, Korea Electric Power Research Institute (KEPRI), Daejeon (Korea, Republic of)

2016-11-15

Separation of CO{sub 2} in the flue gas emitted from coal-fired power plants is the first technological step toward reducing the CO{sub 2} concentration in atmosphere, and eventually for mitigating the global climate change. We could isolate the PZ-dicarbamate, where two CO{sub 2} molecules are bonded to each secondary amine group, through CO{sub 2} absorption by PZ in methanol, and determined its crystal structure by X-ray crystallography. The PZ-dicarbamate as a salt with piperazinium allowed further analyses such as TGA and NMR measurements, which gave information on the fate of the salt. In particular, the salt can be used as a standard sample exhibiting 100% CO{sub 2} loading in a PZ molecule.

Protection of a PWR nuclear power stations against corrosion using hydrogen molecules to capture oxygen molecules

International Nuclear Information System (INIS)

Nahili, M.

2004-01-01

A protection method for the primary loops metals of nuclear power plants from corrosion was investigated. Hydrogen molecules were added to the primary circuit to eliminate oxygen molecules produced by radiolysis of coolant at the reactor core. The hydrogen molecules were produced by electrolyses of water and then added when the coolant water was passing through the primary coolant circuit. Thermodynamical process and the protection methods from corrosion were discussed, the discussion emphasized on the removal of oxygen molecules as one of the protection methods, and compared with other methods. The amount of hydrogen molecules needed for complete removal of oxygen was estimated in two cases: in the case without passing the water through the oxygen removal system, and in the case of passing water through the system. A pressurized water reactor VVER was chosen to be investigated in this study. The amount of hydrogen molecules was estimated so as to eliminate completely the oxygen molecules from coolant water. The estimated value was found to be less than the permissible range for coolant water for such type of reactors. A simulation study for interaction mechanism between hydrogen and oxygen molecules as water flowing in a tube similar to that of coolant water was performed with different water flow velocities. The interaction between the molecules of hydrogen and oxygen was described. The gas diffusion at the surface of the tube was found to play a major role in the interaction. A mathematical model was found to give full description of the change of oxygen concentration through the tube, as well as, to calculate the length of the tube where the concentration of oxygen reduced to few order of magnitude. (Author)

Atomic excitation and molecular dissociation by low energy electron collisions

International Nuclear Information System (INIS)

Weyland, Marvin

2016-01-01

In this work, momentum imaging experiments have been conducted for the electron impact excitation of metastable states in noble gases and for dissociative electron attachment (DEA) in polyatomic molecules. For the electron impact excitation study a new experimental technique has been developed which is able to measure the scattering angle distribution of the electrons by detection of the momentum transfer to the atoms. Momentum transfer images have been recorded for helium and neon at fixed electron impact energy close to the excitation threshold and good agreement with current R-matrix theory calculations was found. A new momentum imaging apparatus for negative ions has been built for the purpose of studying DEA in biologically relevant molecules. During this work, DEA was investigated in the molecules ammonia, water, formic acid, furan, pyridine and in two chlorofluorocarbons. Furthermore, the change of DEA resonance energies when molecules form clusters compared to monomers was investigated in ammonia and formic acid. The experimental results of most studied molecules could be compared to recent theoretical calculations and they support further development in the theoretical description of DEA. The new apparatus built in this work also delivered a superior momentum resolution compared to existing setups. This allows the momentum imaging of heavier fragments and fragments with lower kinetic energy.

An axis-specific rotational rainbow in the direct scatter of formaldehyde from Au(111) and its influence on trapping probability.

Science.gov (United States)

Park, G Barratt; Krüger, Bastian C; Meyer, Sven; Kandratsenka, Alexander; Wodtke, Alec M; Schäfer, Tim

2017-08-02

The conversion of translational to rotational motion often plays a major role in the trapping of small molecules at surfaces, a crucial first step for a wide variety chemical processes that occur at gas-surface interfaces. However, to date most quantum-state resolved surface scattering experiments have been performed on diatomic molecules, and little detailed information is available about how the structure of nonlinear polyatomic molecules influences the mechanisms for energy exchange with surfaces. In the current work, we employ a new rotationally resolved 1 + 1' resonance-enhanced multiphoton ionization (REMPI) scheme to measure the rotational distribution in formaldehyde molecules directly scattered from the Au(111) surface at incidence kinetic energies in the range 0.3-1.2 eV. The results indicate a pronounced propensity to excite a-axis rotation (twirling) rather than b- or c-axis rotation (tumbling or cartwheeling), and are consistent with a rotational rainbow scattering model. Classical trajectory calculations suggest that the effect arises-to zeroth order-from the three-dimensional shape of the molecule (steric effects). Analysis suggests that the high degree of rotational excitation has a substantial influence on the trapping probability of formaldehyde at incidence translational energies above 0.5 eV.

Atomic excitation and molecular dissociation by low energy electron collisions

Energy Technology Data Exchange (ETDEWEB)

Weyland, Marvin

2016-11-16

In this work, momentum imaging experiments have been conducted for the electron impact excitation of metastable states in noble gases and for dissociative electron attachment (DEA) in polyatomic molecules. For the electron impact excitation study a new experimental technique has been developed which is able to measure the scattering angle distribution of the electrons by detection of the momentum transfer to the atoms. Momentum transfer images have been recorded for helium and neon at fixed electron impact energy close to the excitation threshold and good agreement with current R-matrix theory calculations was found. A new momentum imaging apparatus for negative ions has been built for the purpose of studying DEA in biologically relevant molecules. During this work, DEA was investigated in the molecules ammonia, water, formic acid, furan, pyridine and in two chlorofluorocarbons. Furthermore, the change of DEA resonance energies when molecules form clusters compared to monomers was investigated in ammonia and formic acid. The experimental results of most studied molecules could be compared to recent theoretical calculations and they support further development in the theoretical description of DEA. The new apparatus built in this work also delivered a superior momentum resolution compared to existing setups. This allows the momentum imaging of heavier fragments and fragments with lower kinetic energy.

Molecule of the Month

Indian Academy of Sciences (India)

Cyclo bu tadiene (1) has been one of the most popular molecules for experimentalists and theoreticians. This molecule is unstable as . it is antiaromatic ( 4,n electrons in a cyclic array). Even though some highly substituted cyclobutadienes, for example, compound 2 and the Fe(CO)3 complex of cyclobutadiene (3) are ...

Spectroscopy and Chemistry of Cold Molecules

Science.gov (United States)

Momose, Takamasa

2012-06-01

Molecules at low temperatures are expected to behave quite differently from those at high temperatures because pronounced quantum effects emerge from thermal averages. Even at 10 K, a significant enhancement of reaction cross section is expected due to tunneling and resonance effects. Chemistry at this temperature is very important in order to understand chemical reactions in interstellar molecular clouds. At temperatures lower than 1 K, collisions and intermolecular interactions become qualitatively different from those at high temperatures because of the large thermal de Broglie wavelength of molecules. Collisions at these temperatures must be treated as the interference of molecular matter waves, but not as hard sphere collisions. A Bose-Einstein condensate is a significant state of matter as a result of coherent matter wave interaction. Especially, dense para-H_2 molecules are predicted to become a condensate even around 1 K. A convenient method to investigate molecules around 1 K is to dope molecules in cold matrices. Among various matrices, quantum hosts such as solid para-H_2 and superfluid He nano-droplets have been proven to be an excellent host for high-resolution spectroscopy. Rovibrational motion of molecules in these quantum hosts is well quantized on account of the weak interactions and the softness of quantum environment. The linewidths of infrared spectra of molecules in the quantum hosts are extremely narrow compared with those in other matrices. The sharp linewidths allow us to resolve fine spectral structures originated in subtle interactions between guest and host molecules. In this talk, I will describe how the splitting and lineshape of high-resolution spectra of molecules in quantum hosts give us new information on the static and dynamical interactions of molecules in quantum medium. The topics include dynamical response of superfluid environment upon rotational excitation, and possible superfluid phase of para-H_2 clusters. I will also

Isotope separation using vibrationally excited molecules

International Nuclear Information System (INIS)

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

1977-01-01

A system for isotope separation or enrichment wherein molecules of a selected isotope type in a flow of molecules of plural isotope types are vibrationally excited and collided with a background gas to provide enhanced diffusivity for the molecules of the selected isotope type permitting their separate collection. The system typically is for the enrichment of uranium using a uranium hexafluoride gas in combination with a noble gas such as argon. The uranium hexafluoride molecules having a specific isotope of uranium are vibrationally excited by laser radiation. The vibrational energy is converted to a translation energy upon collision with a particle of the background gas and the added translation energy enhances the diffusivity of the selected hexafluoride molecules facilitating its condensation on collection surfaces provided for that purpose. This process is periodically interrupted and the cryogenic flow halted to permit evaporation of the collected molecules to provide a distinct, enriched flow

Effect of irradiation on gene expression of rat liver adhesion molecules. In vivo and in vitro studies

International Nuclear Information System (INIS)

Moriconi, Federico; Malik, Ihtzaz; Ahmad, Ghayyor; Dudas, Joszef; Ramadori, Giuliano; Rave-Fraenk, Margret; Vorwerk, Hilke; Hille, Andrea; Hess, Clemens Friedrich; Christiansen, Hans

2009-01-01

Background and purpose: Migration of leukocytes into tissue is a key element of innate and adaptive immunity. An animal study showed that liver irradiation, in spite of induction of chemokine gene expression, does not lead to recruitment of leukocytes into the parenchyma. The aim of this study was to analyze gene expression of adhesion molecules, which mediate leukocyte recruitment into organs, in irradiated rat liver in vivo and rat hepatocytes in vitro. Material and methods: Rat livers in vivo were irradiated selectively at 25 Gy. Isolated hepatocytes in vitro were irradiated at 8 Gy. RNA extracted within 48 h after irradiation in vivo and in vitro was analyzed by real-time PCR (polymerase chain reaction) and Northern blot. Adhesion molecule concentration in serum was measured by ELISA (enzyme-linked immunosorbent assay). Cryostat sections of livers were used for immunohistology. Results: Significant radiation-induced increase of ICAM-1 (intercellular adhesion molecule-1), VCAM-1 (vascular cell adhesion molecule-1), JAM-1 (junctional adhesion molecule-1), β 1 -integrin, β 2 -integrin, E-cadherin, and P-selectin gene expression could be detected in vivo, while PECAM-1 (platelet-endothelial cell adhesion molecule-1) gene expression remained unchanged. In vitro, β 1 -integrin, JAM-1, and ICAM-2 showed a radiation-induced increased expression, whereas the levels of P-selectin, ICAM-1, PECAM-1, VCAM-1, Madcam-1 (mucosal addressin cell adhesion molecule-1), β 2 -integrin, and E-cadherin were downregulated. However, incubation of irradiated hepatocytes with either tumor necrosis factor-(TNF-)α, interleukin-(IL-)1β, or IL-6 plus TNF-α led to an upregulation of P-selectin, ICAM-1 and VCAM-1. Conclusion: The findings suggest that liver irradiation modulates gene expression of the main adhesion molecules in vivo and in cytokine-activated hepatocytes, with the exception of PECAM-1. This may be one reason for the lack of inflammation in the irradiated rat liver. (orig.)

Trapping molecules in two and three dimensions

International Nuclear Information System (INIS)

Pinkse, PW.H.; Junglen, T.; Rieger, T.; Rangwala, S.A.; Windpassinger, P.; Rempe, G.

2005-01-01

Full text: Cold molecules offer a new testing ground for quantum-physical effects in nature. For example, producing slow beams of large molecules could push experiments studying the boundary between quantum interference and classical particles up towards ever heavier particles. Moreover, cold molecules, in particular YbF, seem an attractive way to narrow down the constraints on the value of the electron dipole moment and finally, quantum information processing using chains of cold polar molecules or vibrational states in molecules have been proposed. All these proposals rely on advanced production and trapping techniques, most of which are still under development. Therefore, novel production and trapping techniques for cold molecules could offer new possibilities not found in previous methods. Electric traps hold promise for deep trap potentials for neutral molecules. Recently we have demonstrated two-dimensional trapping of polar molecules in a four-wire guide using electrostatic and electrodynamic trapping techniques. Filled from a thermal effusive source, such a guide will deliver a beam of slow molecules, which is an ideal source for interferometry experiments with large molecules, for instance. Here we report about the extension of this work to three-dimensional trapping. Polar molecules with a positive Stark shift can be trapped in the minimum of an electrostatic field. We have successfully tested a large volume electrostatic trap for ND3 molecules. A special feature of this trap is that it can be loaded continuously from an electrostatic guide, at a temperature of a few hundred mK. (author)

Moessbauer study of 57Fe isolated in NH3 and NH3/Xe matrices

International Nuclear Information System (INIS)

Saitovitch, E.M.B.; Litterst, F.J.; Micklitz, H.

1981-01-01

Moessbauer studies on 57 Fe isolated in solid ammonia and ammonia/xenon mixtures were perfomed at 4.2 K and 77 K. They show clearly that atomic iron reacts only with one ammonia molecule forming FeNH 3 which is stable in an ammonia matrix up to 77 K. In addition a compound is formed which is attributed to an iron (II) hexammine. (Author) [pt

Standardization of sample collection, isolation and analysis methods in extracellular vesicle research

Directory of Open Access Journals (Sweden)

Kenneth W. Witwer

2013-05-01

Full Text Available The emergence of publications on extracellular RNA (exRNA and extracellular vesicles (EV has highlighted the potential of these molecules and vehicles as biomarkers of disease and therapeutic targets. These findings have created a paradigm shift, most prominently in the field of oncology, prompting expanded interest in the field and dedication of funds for EV research. At the same time, understanding of EV subtypes, biogenesis, cargo and mechanisms of shuttling remains incomplete. The techniques that can be harnessed to address the many gaps in our current knowledge were the subject of a special workshop of the International Society for Extracellular Vesicles (ISEV in New York City in October 2012. As part of the “ISEV Research Seminar: Analysis and Function of RNA in Extracellular Vesicles (evRNA”, 6 round-table discussions were held to provide an evidence-based framework for isolation and analysis of EV, purification and analysis of associated RNA molecules, and molecular engineering of EV for therapeutic intervention. This article arises from the discussion of EV isolation and analysis at that meeting. The conclusions of the round table are supplemented with a review of published materials and our experience. Controversies and outstanding questions are identified that may inform future research and funding priorities. While we emphasize the need for standardization of specimen handling, appropriate normative controls, and isolation and analysis techniques to facilitate comparison of results, we also recognize that continual development and evaluation of techniques will be necessary as new knowledge is amassed. On many points, consensus has not yet been achieved and must be built through the reporting of well-controlled experiments.

Theoretical Investigations Regarding Single Molecules

DEFF Research Database (Denmark)

Pedersen, Kim Georg Lind

Neoclassical Valence Bond Theory, Quantum Transport, Quantum Interference, Kondo Effect, and Electron Pumping. Trap a single organic molecule between two electrodes and apply a bias voltage across this "molecular junction". When electrons pass through the molecule, the different electron paths can...... interfere destructively or constructively. Destructive interference effects in electron transport could potentially improve thermo-electrics, organic logic circuits and energy harvesting. We have investigated destructive interference in off-resonant transport through organic molecules, and have found a set...

Infrared Multiphoton Dissociation Spectroscopy with Free-Electron Lasers: On the Road from Small Molecules to Biomolecules.

Science.gov (United States)

Jašíková, Lucie; Roithová, Jana

2018-03-07

Infrared multiphoton dissociation (IRMPD) spectroscopy is commonly used to determine the structure of isolated, mass-selected ions in the gas phase. This method has been widely used since it became available at free-electron laser (FEL) user facilities. Thus, in this Minireview, we examine the use of IRMPD/FEL spectroscopy for investigating ions derived from small molecules, metal complexes, organometallic compounds and biorelevant ions. Furthermore, we outline new applications of IRMPD spectroscopy to study biomolecules. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Importance of the alignment of polar π conjugated molecules inside carbon nanotubes in determining second-order non-linear optical properties.

Science.gov (United States)

Yumura, Takashi; Yamamoto, Wataru

2017-09-20

We employed density functional theory (DFT) calculations with dispersion corrections to investigate energetically preferred alignments of certain p,p'-dimethylaminonitrostilbene (DANS) molecules inside an armchair (m,m) carbon nanotube (n × DANS@(m,m)), where the number of inner molecules (n) is no greater than 3. Here, three types of alignments of DANS are considered: a linear alignment in a parallel fashion and stacking alignments in parallel and antiparallel fashions. According to DFT calculations, a threshold tube diameter for containing DANS molecules in linear or stacking alignments was found to be approximately 1.0 nm. Nanotubes with diameters smaller than 1.0 nm result in the selective formation of linearly aligned DANS molecules due to strong confinement effects within the nanotubes. By contrast, larger diameter nanotubes allow DANS molecules to align in a stacking and linear fashion. The type of alignment adopted by the DANS molecules inside a nanotube is responsible for their second-order non-linear optical properties represented by their static hyperpolarizability (β 0 values). In fact, we computed β 0 values of DANS assemblies taken from optimized n × DANS@(m,m) structures, and their values were compared with those of a single DANS molecule. DFT calculations showed that β 0 values of DANS molecules depend on their alignment, which decrease in the following order: linear alignment > parallel stacking alignment > antiparallel stacking alignment. In particular, a linear alignment has a β 0 value more significant than that of the same number of isolated molecules. Therefore, the linear alignment of DANS molecules, which is only allowed inside smaller diameter nanotubes, can strongly enhance their second-order non-linear optical properties. Since the nanotube confinement determines the alignment of DANS molecules, a restricted nanospace can be utilized to control their second-order non-linear optical properties. These DFT findings can assist in the

Isolation and characterization of chicken and turkey beta 2-microglobulin

DEFF Research Database (Denmark)

Skjødt, K; Welinder, K G; Crone, M

1986-01-01

Chicken and turkey beta 2-m were isolated from citrated plasma in sequential use of three chromatographic steps: affinity chromatography, gel filtration chromatography and anion-exchange chromatography. The purified protein was identified as beta 2-m by reaction with a beta 2-m specific monoclonal...... (turkey migrates in the alpha and chicken migrates in the beta region). The mol. wt of both chicken and turkey beta 2-m was 14,500 estimated by SDS-PAGE whereas calculations based on the amino acid compositions gave mol. wts of 11,000. EM280 was 15.9 for chicken beta 2-m and 16.4 for turkey beta 2-m......, and is incompatible with a previously published sequence also thought to be from turkey beta 2-m. Reasons for our opinion that the molecules isolated and sequenced in this paper are the correct ones are given. Udgivelsesdato: 1986-Dec...

Isolation of bacterial extrachromosomal DNA from human dental plaque associated with periodontal disease, using transposon-aided capture (TRACA).

Science.gov (United States)

Warburton, Philip J; Allan, Elaine; Hunter, Stephanie; Ward, John; Booth, Veronica; Wade, William G; Mullany, Peter

2011-11-01

The human oral cavity is host to a complex microbial community estimated to comprise >700 bacterial species, of which at least half are thought to be not yet cultivable in vitro. To investigate the plasmids present in this community, we used a transposon-aided capture system, which allowed the isolation of plasmids from human oral supra- and subgingival plaque samples. Thirty-two novel plasmids and a circular molecule that could be an integrase-generated circular intermediate were isolated. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Electron-molecule interactions and their applications

CERN Document Server

Christophorou, L G

1984-01-01

Electron-Molecule Interactions and Their Applications, Volume 2 provides a balanced and comprehensive account of electron-molecule interactions in dilute and dense gases and liquid media. This book consists of six chapters. Chapter 1 deals with electron transfer reactions, while Chapter 2 discusses electron-molecular positive-ion recombination. The electron motion in high-pressure gases and electron-molecule interactions from single- to multiple-collision conditions is deliberated in Chapter 3. In Chapter 4, knowledge on electron-molecule interactions in gases is linked to that on similar proc

Unusual Multiple Production of N-Acylhomoserine Lactones a by Burkholderia sp. Strain C10B Isolated from Dentine Caries

Directory of Open Access Journals (Sweden)

Share Yuan Goh

2014-05-01

Full Text Available Bacteria realize the ability to communicate by production of quorum sensing (QS molecules called autoinducers, which regulate the physiological activities in their ecological niches. The oral cavity could be a potential area for the presence of QS bacteria. In this study, we report the isolation of a QS bacterial isolate C10B from dentine caries. Preliminary screening using Chromobacterium violaceum CV026 biosensor showed that isolate C10B was able to produce N-acylhomoserine lactones (AHLs. This bacterium was further identified as a member of Burkholderia, an opportunistic pathogen. The isolated Burkholderia sp. was confirmed to produce N-hexanoyl-L-homoserine lactone (C6-HSL, N-octanoyl-L-homoserine lactone (C8-HSL, N-decanoyl-L-homoserine lactone (C10-HSL and N-dodecanoyl-L-homoserine lactone (C12-HSL.

Domain-based small molecule binding site annotation

Directory of Open Access Journals (Sweden)

Dumontier Michel

2006-03-01

Full Text Available Abstract Background Accurate small molecule binding site information for a protein can facilitate studies in drug docking, drug discovery and function prediction, but small molecule binding site protein sequence annotation is sparse. The Small Molecule Interaction Database (SMID, a database of protein domain-small molecule interactions, was created using structural data from the Protein Data Bank (PDB. More importantly it provides a means to predict small molecule binding sites on proteins with a known or unknown structure and unlike prior approaches, removes large numbers of false positive hits arising from transitive alignment errors, non-biologically significant small molecules and crystallographic conditions that overpredict ion binding sites. Description Using a set of co-crystallized protein-small molecule structures as a starting point, SMID interactions were generated by identifying protein domains that bind to small molecules, using NCBI's Reverse Position Specific BLAST (RPS-BLAST algorithm. SMID records are available for viewing at http://smid.blueprint.org. The SMID-BLAST tool provides accurate transitive annotation of small-molecule binding sites for proteins not found in the PDB. Given a protein sequence, SMID-BLAST identifies domains using RPS-BLAST and then lists potential small molecule ligands based on SMID records, as well as their aligned binding sites. A heuristic ligand score is calculated based on E-value, ligand residue identity and domain entropy to assign a level of confidence to hits found. SMID-BLAST predictions were validated against a set of 793 experimental small molecule interactions from the PDB, of which 472 (60% of predicted interactions identically matched the experimental small molecule and of these, 344 had greater than 80% of the binding site residues correctly identified. Further, we estimate that 45% of predictions which were not observed in the PDB validation set may be true positives. Conclusion By

Isolation and characterization of biosurfactant producing bacteria from Persian Gulf (Bushehr provenance)

International Nuclear Information System (INIS)

Hassanshahian, Mehdi

2014-01-01

Highlights: • Biosurfactant producing bacteria were isolated from Persian Gulf. • There is high diversity of biosurfactant producing bacteria in the Persian Gulf. • These bacteria are very useful for management of oil pollution in the sea. - Abstract: Biosurfactants are surface active materials that are produced by some microorganisms. These molecules increase biodegradation of insoluble pollutants. In this study sediments and seawater samples were collected from the coastline of Bushehr provenance in the Persian Gulf and their biosurfactant producing bacteria were isolated. Biosurfactant producing bacteria were isolated by using an enrichment method in Bushnell-Hass medium with diesel oil as the sole carbon source. Five screening tests were used for selection of Biosurfactant producing bacteria: hemolysis in blood agar, oil spreading, drop collapse, emulsification activity and Bacterial Adhesion to Hydrocarbon test (BATH). These bacteria were identified using biochemical and molecular methods. Eighty different colonies were isolated from the collected samples. The most biosurfactant producing isolates related to petrochemical plants of Khark Island. Fourteen biosurfactant producing bacteria were selected between these isolates and 7 isolates were screened as these were predominant producers that belong to Shewanella alga, Shewanella upenei, Vibrio furnissii, Gallaecimonas pentaromativorans, Brevibacterium epidermidis, Psychrobacter namhaensis and Pseudomonas fluorescens. The largest clear zone diameters in oil spreading were observed for G. pentaromativorans strain O15. Also, this strain has the best emulsification activity and reduction of surface tension, suggesting it is the best of thee isolated strains. The results of this study confirmed that there is high diversity of biosurfactant producing bacteria in marine ecosystem of Iran and by application of these bacteria in petrochemical waste water environmental problems can be assisted

Interstellar Molecules

Science.gov (United States)

Solomon, Philip M.

1973-01-01

Radioastronomy reveals that clouds between the stars, once believed to consist of simple atoms, contain molecules as complex as seven atoms and may be the most massive objects in our Galaxy. (Author/DF)

Electrochemically-gated single-molecule electrical devices

International Nuclear Information System (INIS)

Guo, Shaoyin; Artés, Juan Manuel; Díez-Pérez, Ismael

2013-01-01

In the last decade, single-molecule electrical contacts have emerged as a new experimental platform that allows exploring charge transport phenomena in individual molecular blocks. This novel tool has evolved into an essential element within the Molecular Electronics field to understand charge transport processes in hybrid (bio)molecule/electrode interfaces at the nanoscale, and prospect the implementation of active molecular components into functional nanoscale optoelectronic devices. Within this area, three-terminal single-molecule devices have been sought, provided that they are highly desired to achieve full functionality in logic electronic circuits. Despite the latest experimental developments offer consistent methods to bridge a molecule between two electrodes (source and drain in a transistor notation), placing a third electrode (gate) close to the single-molecule electrical contact is still technically challenging. In this vein, electrochemically-gated single-molecule devices have emerged as an experimentally affordable alternative to overcome these technical limitations. In this review, the operating principle of an electrochemically-gated single-molecule device is presented together with the latest experimental methodologies to built them and characterize their charge transport characteristics. Then, an up-to-date comprehensive overview of the most prominent examples will be given, emphasizing on the relationship between the molecular structure and the final device electrical behaviour

Insights into the role of protein molecule size and structure on interfacial properties using designed sequences

Science.gov (United States)

Dwyer, Mirjana Dimitrijev; He, Lizhong; James, Michael; Nelson, Andrew; Middelberg, Anton P. J.

2013-01-01

Mixtures of a large, structured protein with a smaller, unstructured component are inherently complex and hard to characterize at interfaces, leading to difficulties in understanding their interfacial behaviours and, therefore, formulation optimization. Here, we investigated interfacial properties of such a mixed system. Simplicity was achieved using designed sequences in which chemical differences had been eliminated to isolate the effect of molecular size and structure, namely a short unstructured peptide (DAMP1) and its longer structured protein concatamer (DAMP4). Interfacial tension measurements suggested that the size and bulk structuring of the larger molecule led to much slower adsorption kinetics. Neutron reflectometry at equilibrium revealed that both molecules adsorbed as a monolayer to the air–water interface (indicating unfolding of DAMP4 to give a chain of four connected DAMP1 molecules), with a concentration ratio equal to that in the bulk. This suggests the overall free energy of adsorption is equal despite differences in size and bulk structure. At small interfacial extensional strains, only molecule packing influenced the stress response. At larger strains, the effect of size became apparent, with DAMP4 registering a higher stress response and interfacial elasticity. When both components were present at the interface, most stress-dissipating movement was achieved by DAMP1. This work thus provides insights into the role of proteins' molecular size and structure on their interfacial properties, and the designed sequences introduced here can serve as effective tools for interfacial studies of proteins and polymers. PMID:23303222

Targeting Jurkat T Lymphocyte Leukemia Cells by an Engineered Interferon-Alpha Hybrid Molecule

Directory of Open Access Journals (Sweden)

Dehai Yu

2017-06-01

Full Text Available Background/Aims: Adult T-cell leukemia/lymphoma (ATL is a very aggressive T cell malignancy that carries a poor prognosis, primarily due to its resistance to chemotherapy and to life-threatening infectious complications. Interferon-alpha (IFNα has been used in combination with the anti-retroviral drug zidovudine to treat patients with ATL. However, the efficacy of long-term therapy is significantly limited due to the systemic toxicity of IFNα. Methods: We utilized phage display library screening to identify short peptides that specifically bind to Jurkat T lymphocyte leukemia cells. By fusing the Jurkat-binding peptide to the C-terminus of IFNα, we constructed an engineered chimeric IFNα molecule (IFNP for the treatment of ATL. Results: We found that IFNP exhibited significantly higher activity than wild type IFNα in inhibiting the growth of leukemia cells and inducing cell blockage at the G0/G1 phase. The synthetic IFNP molecule exerted its antitumor activity by upregulating the downstream genes involved in the STAT1 pathway and in apoptosis. Using a cell receptor binding assay, we showed that this Jurkat-binding peptide facilitated the binding affinity of IFNα to the cell surface type I IFN receptor. Conclusion: The isolated Jurkat-binding peptide significantly potentiates the therapeutic activity of IFNα in T lymphocyte leukemia cells. The engineered IFNP molecule may prove to a novel antitumor approach in the treatment of patients with ATL.

Vibrational spectroscopy and structural analysis of uranium complexes

Energy Technology Data Exchange (ETDEWEB)

Umrejko, D.S.; Nikanovich, M.V.

1984-12-01

On the basis of experimental and theoretical studies of vibbrational spectra for halides, sulfates, phosphates, uranyl oxalates (and uranium) as well as for more complicated complex systems, reliable spectroscopic criteria have been established for estimation of their structural features by more simple and accessible (than direct) methods. Due to coordination to a central ion of U/sup 6/(U/sup 4/) ligands a geometry variation specific for each method of addition occurs and concomitant redistribution of the force interaction in the mentioned system as well, which directly affects the variation of their frequency characteristics and vibration modes. On this ground stable indications of particular types of coordination for mono- and polyatomic groups (including bridge-type, characteristic of polymetric structures) are pointed out in the IR absorption and Raman spectra. In the investigated structures the predominant effect of coordination on the spectral properties of complexes, as compared with other factors (for example, outer-sphere binding) is established. The presence of water molecules in an interlayer space does not tell essentially on the state of polyatomic ligands with all donor atoms bound with the uranium central atom (particularly, in binary uranyl phosphates). In the presence of free oxygen atoms the H/sub 2/O effect can lead only to some shift of the maxima of separate bands and their additional weak splitting (in uranyl sulfates).

Decline of the self-focusing of a pulsed high intensity electron beam owing to gas breakdown

International Nuclear Information System (INIS)

Hotta, H.; Arai, H.

1977-01-01

The self-focusing of a pulsed high-intensity electron beam in a gas declines in the intermediate pressure region owing to gas breakdown. The degree of the self-focusing of a beam from a Febetron 706 in monatomic gases increases by increasing the breakdown time (t/sub B/), which is defined as the time when the plasma conductivity becomes 10 mho/cm. Secondary electrons are consumed appreciably in polyatomic gases after t/sub B/ through their reactions with ions and neutral molecules. Therefore, in such gases, the amount of the consumption must be estimated to analyze the self-focusing. For the estimation of the consumption, we must remark that the mean energy of secondary electrons is quite different between before and after t/sub B/ because of the different strength of induced longitudinal electric field. As a result of the numerical analyses, we obtain the equation t/sub B/-t/sub N/ =12/w (α-eta) (t/sub N/ is neutralization time, w is electron drift velocity, α is the first Townsend ionization coefficient, and eta is the electron attachment coefficient). Since eta is usually negligibly small before t/sub B/ and t/sub N/ is also negligibly small above a certain pressure, t/sub B/ is approximately inversely proportional to wα. The t/sub B/ in polyatomic gases, however, must be corrected for the consumption described above

Constructing polyatomic potential energy surfaces by interpolating diabatic Hamiltonian matrices with demonstration on green fluorescent protein chromophore

Energy Technology Data Exchange (ETDEWEB)

Park, Jae Woo; Rhee, Young Min, E-mail: ymrhee@postech.ac.kr [Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang 790-784 (Korea, Republic of); Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 790-784 (Korea, Republic of)

2014-04-28

Simulating molecular dynamics directly on quantum chemically obtained potential energy surfaces is generally time consuming. The cost becomes overwhelming especially when excited state dynamics is aimed with multiple electronic states. The interpolated potential has been suggested as a remedy for the cost issue in various simulation settings ranging from fast gas phase reactions of small molecules to relatively slow condensed phase dynamics with complex surrounding. Here, we present a scheme for interpolating multiple electronic surfaces of a relatively large molecule, with an intention of applying it to studying nonadiabatic behaviors. The scheme starts with adiabatic potential information and its diabatic transformation, both of which can be readily obtained, in principle, with quantum chemical calculations. The adiabatic energies and their derivatives on each interpolation center are combined with the derivative coupling vectors to generate the corresponding diabatic Hamiltonian and its derivatives, and they are subsequently adopted in producing a globally defined diabatic Hamiltonian function. As a demonstration, we employ the scheme to build an interpolated Hamiltonian of a relatively large chromophore, para-hydroxybenzylidene imidazolinone, in reference to its all-atom analytical surface model. We show that the interpolation is indeed reliable enough to reproduce important features of the reference surface model, such as its adiabatic energies and derivative couplings. In addition, nonadiabatic surface hopping simulations with interpolation yield population transfer dynamics that is well in accord with the result generated with the reference analytic surface. With these, we conclude by suggesting that the interpolation of diabatic Hamiltonians will be applicable for studying nonadiabatic behaviors of sizeable molecules.

FlavorDB: a database of flavor molecules.

Science.gov (United States)

Garg, Neelansh; Sethupathy, Apuroop; Tuwani, Rudraksh; Nk, Rakhi; Dokania, Shubham; Iyer, Arvind; Gupta, Ayushi; Agrawal, Shubhra; Singh, Navjot; Shukla, Shubham; Kathuria, Kriti; Badhwar, Rahul; Kanji, Rakesh; Jain, Anupam; Kaur, Avneet; Nagpal, Rashmi; Bagler, Ganesh

2018-01-04

Flavor is an expression of olfactory and gustatory sensations experienced through a multitude of chemical processes triggered by molecules. Beyond their key role in defining taste and smell, flavor molecules also regulate metabolic processes with consequences to health. Such molecules present in natural sources have been an integral part of human history with limited success in attempts to create synthetic alternatives. Given their utility in various spheres of life such as food and fragrances, it is valuable to have a repository of flavor molecules, their natural sources, physicochemical properties, and sensory responses. FlavorDB (http://cosylab.iiitd.edu.in/flavordb) comprises of 25,595 flavor molecules representing an array of tastes and odors. Among these 2254 molecules are associated with 936 natural ingredients belonging to 34 categories. The dynamic, user-friendly interface of the resource facilitates exploration of flavor molecules for divergent applications: finding molecules matching a desired flavor or structure; exploring molecules of an ingredient; discovering novel food pairings; finding the molecular essence of food ingredients; associating chemical features with a flavor and more. Data-driven studies based on FlavorDB can pave the way for an improved understanding of flavor mechanisms. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Engineering and control of cold molecules. Making manipulating and exploiting ultra-cold polar molecules

International Nuclear Information System (INIS)

Bigelow, N.P.; Haimberger, C.; Kleinert, J.; Tscherneck, M.; Holmes, M.E.

2005-01-01

In the last 12 months several groups have demonstrated the use of photo association to create cold heteronuclear (polar) molecules. We report on the formation of translationally cold NaCs molecules starting from a laser-cooled atomic vapor of Na and Cs atoms. Colliding atoms are transferred into bound molecular states in a two-step photoactivated process. We find a translational temperature of T ≅ 260 mK. To increase the density and number of trapped atoms, dark-spot techniques are used on the MOT and a Zeeman slowed sodium beam is used to load the sodium atoms into the trap. Spectroscopy of these molecules is underway using time-of-flight ion detection and trap-loss. Initial REMPI measurements indicate that both singlet and triplet states are being populated by the spontaneous-decay driven process. We measure a rate constant for molecule formation of K NaCs = 7.43 · 10 15 cm 3 s -1 . (author)

Formation of ultracold NaRb Feshbach molecules

International Nuclear Information System (INIS)

Wang, Fudong; He, Xiaodong; Li, Xiaoke; Zhu, Bing; Chen, Jun; Wang, Dajun

2015-01-01

We report the creation of ultracold bosonic 23 Na 87 Rb Feshbach molecules via magneto-association. By ramping the magnetic field across an interspecies Feshbach resonance (FR), at least 4000 molecules can be produced out of the near degenerate ultracold mixture. Fast loss due to inelastic atom–molecule collisions is observed, which limits the pure molecule number, after residual atoms removal, to 1700. The pure molecule sample can live for 21.8(8) ms in the optical trap, long enough for future molecular spectroscopy studies toward coherently transferring to the singlet ro-vibrational ground state, where these molecules are stable against chemical reaction and have a permanent electric dipole moment of 3.3 Debye. We have also measured the Feshbach molecule’s binding energy near the FR by the oscillating magnetic field method and found these molecules have a large closed-channel fraction. (paper)

Quantum transport through organic molecules

International Nuclear Information System (INIS)

Maiti, Santanu K.

2007-01-01

We investigate the electronic transport for the model of benzene-1, 4-dithiolate (BDT) molecule and some other geometric models of benzene molecule attached with two semi-infinite metallic electrodes by the use of Green's function technique. An analytic approach for the electronic transport through the molecular bridges is presented, based on the tight-binding model. Transport of electrons in such molecular bridges is strongly affected by the geometry of the molecules and their coupling strength with the electrodes. Conductance (g) shows resonance peaks associated with the molecular energy eigenstates. In the weak molecule-to-electrodes coupling limit current (I) passing through the molecules shows staircase-like behavior with sharp steps, while, it varies quite continuously in the limit of strong molecular coupling with the applied bias voltage (V). In presence of the transverse magnetic field conductance gives oscillatory behavior with flux φ, threaded by the molecular ring, showing φ 0 ( = ch/e) flux-quantum periodicity. Though conductance changes with the application of transverse magnetic field, but the current-voltage characteristics remain same in presence of this magnetic field for these molecular bridge systems

Fluorescent Biosensors Based on Single-Molecule Counting.

Science.gov (United States)

Ma, Fei; Li, Ying; Tang, Bo; Zhang, Chun-Yang

2016-09-20

Biosensors for highly sensitive, selective, and rapid quantification of specific biomolecules make great contributions to biomedical research, especially molecular diagnostics. However, conventional methods for biomolecular assays often suffer from insufficient sensitivity and poor specificity. In some case (e.g., early disease diagnostics), the concentration of target biomolecules is too low to be detected by these routine approaches, and cumbersome procedures are needed to improve the detection sensitivity. Therefore, there is an urgent need for rapid and ultrasensitive analytical tools. In this respect, single-molecule fluorescence approaches may well satisfy the requirement and hold promising potential for the development of ultrasensitive biosensors. Encouragingly, owing to the advances in single-molecule microscopy and spectroscopy over past decades, the detection of single fluorescent molecule comes true, greatly boosting the development of highly sensitive biosensors. By in vitro/in vivo labeling of target biomolecules with proper fluorescent tags, the quantification of certain biomolecule at the single-molecule level is achieved. In comparison with conventional ensemble measurements, single-molecule detection-based analytical methods possess the advantages of ultrahigh sensitivity, good selectivity, rapid analysis time, and low sample consumption. Consequently, single-molecule detection may be potentially employed as an ideal analytical approach to quantify low-abundant biomolecules with rapidity and simplicity. In this Account, we will summarize our efforts for developing a series of ultrasensitive biosensors based on single-molecule counting. Single-molecule counting is a member of single-molecule detection technologies and may be used as a very simple and ultrasensitive method to quantify target molecules by simply counting the individual fluorescent bursts. In the fluorescent sensors, the signals of target biomolecules may be translated to the

Crystal chemistry of uranyl carboxylate coordination networks obtained in the presence of organic amine molecules

Energy Technology Data Exchange (ETDEWEB)

Mihalcea, Ionut; Henry, Natacha; Loiseau, Thierry [Unite de Catalyse et Chimie du Solide (UCCS) - UMR CNRS 8181, Universite de Lille Nord de France, USTL-ENSCL, Villeneuve d' Ascq (France)

2014-03-15

Three uranyl isophthalates (1,3-bdc) and two uranyl pyromellitates (btec) of coordination-polymer type were hydrothermally synthesized (200 C for 24 h) in the presence of different amine-based molecules [1,3-diaminopropane (dap) or dimethylamine (dma) originating from the in situ decomposition of N,N-dimethylformamide]. (UO{sub 2}){sub 2}(OH){sub 2}(H{sub 2}O)(1,3-bdc).H{sub 2}O (1) is composed of inorganic tetranuclear cores, which are linked to each other through the isophthalato ligand to generate infinite neutral ribbons, which are intercalated by free H{sub 2}O molecules. The compounds (UO{sub 2}){sub 1.5}(H{sub 2}O)(1,3-bdc){sub 2}.0.5H{sub 2}dap.1.5H{sub 2}O (2) and UO{sub 2}(1,3-bdc){sub 1.5}.0.5H{sub 2}dap.2H{sub 2}O (3) consist of discrete uranyl-centered hexagonal bipyramids connected to each other by a ditopic linker to form a single-layer network for 2 or a double-layer network for 3. The protonated diamine molecules are located between the uranyl-organic sheets and balance the negative charge of the layered sub-networks. The phase (UO{sub 2}){sub 2}O(btec).2Hdma.H{sub 2}O (4) presents a 2D structure built up from tetranuclear units, which consist of two central sevenfold coordinated uranium centers and two peripheral eightfold coordinated uranium centers. The connection of the resulting tetramers through the pyromellitate molecules generates an anionic layerlike structure, in which the protonated dimethylammonium species are inserted. The compound UO{sub 2}(btec).2Hdma (5) is also a lamellar coordination polymer, which contains isolated eightfold coordinated uranium cations linked through pyromellitate molecules and intercalated by protonated dimethylammonium species. In both phases 4 and 5, the btec linker has non-bonded carboxyl oxygen atoms, which preferentially interact with the protonated amine molecules through a hydrogen-bond network. The different illustrations show the structural diversity of uranyl-organic coordination polymers with organic

Dissociation of NH3 and NH2D by high power CO2 laser radiation

International Nuclear Information System (INIS)

Jacobs, R.R.

1976-08-01

Multiquantum dissociation of polyatomics using intense CO 2 lasers resulting in isotopic enrichment has been demonstrated for several molecules. In this presentation, the possibility of selective dissociation of NH 3 and NH 2 D by high power laser radiation at 10 μm will be considered. Relevant work performed at the Lawrence Livermore Laboratory and elsewhere will be summarized. In this review, attention will be given to four distinct mechanisms that can play varying degrees of importance in such investigations. Discussion will deal with the usefulness of two-resonant-frequency molecular excitation, the role of buffer gases, and the need to monitor the yields into the ground and excited electronic states of the dissociated fragments

Molecule-oriented programming in Java

NARCIS (Netherlands)

Bergstra, J.A.

2002-01-01

Molecule-oriented programming is introduced as a programming style carrying some perspective for Java. A sequence of examples is provided. Supporting the development of the molecule-oriented programming style several matters are introduced and developed: profile classes allowing the representation

MOLECULES IN η CARINAE

International Nuclear Information System (INIS)

Loinard, Laurent; Menten, Karl M.; Güsten, Rolf; Zapata, Luis A.; Rodríguez, Luis F.

2012-01-01

We report the detection toward η Carinae of six new molecules, CO, CN, HCO + , HCN, HNC, and N 2 H + , and of two of their less abundant isotopic counterparts, 13 CO and H 13 CN. The line profiles are moderately broad (∼100 km s –1 ), indicating that the emission originates in the dense, possibly clumpy, central arcsecond of the Homunculus Nebula. Contrary to previous claims, CO and HCO + do not appear to be underabundant in η Carinae. On the other hand, molecules containing nitrogen or the 13 C isotope of carbon are overabundant by about one order of magnitude. This demonstrates that, together with the dust responsible for the dimming of η Carinae following the Great Eruption, the molecules detected here must have formed in situ out of CNO-processed stellar material.

Preparation and isolation of dithiolene thiophosphoryl molecules as stable, protected forms of dithiolene ligands.

Science.gov (United States)

Arumugam, Kuppuswamy; Bollinger, James E; Fink, Mark; Donahue, James P

2007-04-16

The reaction of P4S10 with acyloins, RC(O)CH(OH)R, in refluxing dioxane, followed by the addition of alkylating agents, forms dithiolene thiophosphoryl thiolate compounds, (R2C2S2)P(S)(SR'), which are readily isolated and purified. The compounds that have been prepared and identified spectroscopically are those with R = p-anisyl, R' = Me (1); R = p-anisyl, R' = Bz (2); R = Ph, R' = Me (4); R = Et, R' = Bz (5). Compounds 1, 2, and 4 were structurally characterized by X-ray crystallography and found to possess a tetrahedral coordination geometry about the phosphorus atom, with overall Cs symmetry. In each case, the mirror plane bisects the dithiolene S-P-S chelate and contains the thiophosphoryl bond, which ranges in length from 1.9241(8) to 1.9361(7) A. The use of 2-(bromomethyl)naphthalene as organic electrophile in the P4S10/acyloin reaction produced bis(2-methylnaphthalenyl) disulfide as the only identifiable product. The substitution of Lawesson's reagent for P4S10 in reactions with acyloins produced deoxy acyloin rather than products resulting from chalcogen exchange. Compounds 1-2 and 4-5 are Group 5 analogues of 1,3-dithiol-2-ones, (R2C2S2)C=O, and undergo a similar hydrolysis in aqueous base to liberate ene-1,2-dithiolate dianions from which corresponding metal dithiolene complexes may be prepared. Deprotection of 1 in MeO-/MeOH, followed by the addition of NiCl2.6H2O and then I2, produces square planar [Ni(S2C2(C6H4-p-OCH3)2)2] (8) in 93% yield. A high-resolution structure of 8 (P) reveals dithiolene C-C and C-S bond lengths that are clearly indicative of the thionyl radical monoanionic nature of the ligand. The use of isolated (R2C2S2)P(S)(SR') compounds as a dithiolene ligand source for the preparation of metal dithiolene complexes offers the advantages of clean reactivity and high yield.

Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data.

Science.gov (United States)

Greenfeld, Max; van de Meent, Jan-Willem; Pavlichin, Dmitri S; Mabuchi, Hideo; Wiggins, Chris H; Gonzalez, Ruben L; Herschlag, Daniel

2015-01-16

Single-molecule techniques have emerged as incisive approaches for addressing a wide range of questions arising in contemporary biological research [Trends Biochem Sci 38:30-37, 2013; Nat Rev Genet 14:9-22, 2013; Curr Opin Struct Biol 2014, 28C:112-121; Annu Rev Biophys 43:19-39, 2014]. The analysis and interpretation of raw single-molecule data benefits greatly from the ongoing development of sophisticated statistical analysis tools that enable accurate inference at the low signal-to-noise ratios frequently associated with these measurements. While a number of groups have released analysis toolkits as open source software [J Phys Chem B 114:5386-5403, 2010; Biophys J 79:1915-1927, 2000; Biophys J 91:1941-1951, 2006; Biophys J 79:1928-1944, 2000; Biophys J 86:4015-4029, 2004; Biophys J 97:3196-3205, 2009; PLoS One 7:e30024, 2012; BMC Bioinformatics 288 11(8):S2, 2010; Biophys J 106:1327-1337, 2014; Proc Int Conf Mach Learn 28:361-369, 2013], it remains difficult to compare analysis for experiments performed in different labs due to a lack of standardization. Here we propose a standardized single-molecule dataset (SMD) file format. SMD is designed to accommodate a wide variety of computer programming languages, single-molecule techniques, and analysis strategies. To facilitate adoption of this format we have made two existing data analysis packages that are used for single-molecule analysis compatible with this format. Adoption of a common, standard data file format for sharing raw single-molecule data and analysis outcomes is a critical step for the emerging and powerful single-molecule field, which will benefit both sophisticated users and non-specialists by allowing standardized, transparent, and reproducible analysis practices.

Affinity imaging mass spectrometry (AIMS): high-throughput screening for specific small molecule interactions with frozen tissue sections.

Science.gov (United States)

Yoshimi, T; Kawabata, S; Taira, S; Okuno, A; Mikawa, R; Murayama, S; Tanaka, K; Takikawa, O

2015-11-07

A novel screening system, using affinity imaging mass spectrometry (AIMS), has been developed to identify protein aggregates or organ structures in unfixed human tissue. Frozen tissue sections are positioned on small (millimetre-scale) stainless steel chips and incubated with an extensive library of small molecules. Candidate molecules showing specific affinity for the tissue section are identified by imaging mass spectrometry (IMS). As an example application, we screened over a thousand compounds against Alzheimer's disease (AD) brain tissue and identified several compounds with high affinity for AD brain sections containing tau deposits compared to age-matched controls. It should also be possible to use AIMS to isolate chemical compounds with affinity for tissue structures or components that have been extensively modified by events such as oxidation, phosphorylation, acetylation, aggregation, racemization or truncation, for example, due to aging. It may also be applicable to biomarker screening programs.

Rovibrational spectroscopy using a kinetic energy operator in Eckart frame and the multi-configuration time-dependent Hartree (MCTDH) approach

International Nuclear Information System (INIS)