linear polyatomic molecules: Topics by Science.gov

Sample records for linear polyatomic molecules

Method for preparation and readout of polyatomic molecules in single quantum states

NASA Astrophysics Data System (ADS)

Patterson, David

2018-03-01

Polyatomic molecular ions contain many desirable attributes of a useful quantum system, including rich internal degrees of freedom and highly controllable coupling to the environment. To date, the vast majority of state-specific experimental work on molecular ions has concentrated on diatomic species. The ability to prepare and read out polyatomic molecules in single quantum states would enable diverse experimental avenues not available with diatomics, including new applications in precision measurement, sensitive chemical and chiral analysis at the single-molecule level, and precise studies of Hz-level molecular tunneling dynamics. While cooling the motional state of a polyatomic ion via sympathetic cooling with a laser-cooled atomic ion is straightforward, coupling this motional state to the internal state of the molecule has proven challenging. Here we propose a method for readout and projective measurement of the internal state of a trapped polyatomic ion. The method exploits the rich manifold of technically accessible rotational states in the molecule to realize robust state preparation and readout with far less stringent engineering than quantum logic methods recently demonstrated on diatomic molecules. The method can be applied to any reasonably small (≲10 atoms) polyatomic ion with an anisotropic polarizability.
Overset grid implementation of the complex Kohn variational method for electron-polyatomic molecule scattering

NASA Astrophysics Data System (ADS)

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

2017-04-01

The complex Kohn variational method, which represents the continuum wave function in each channel using a combination of Gaussians and Bessel or Coulomb functions, has been successful in numerous applications to electron-polyatomic molecule scattering and molecular photoionization. The hybrid basis representation limits it to relatively low energies (< 50 eV) , requires an approximation to exchange matrix elements involving continuum functions, and hampers its coupling to modern electronic structure codes for the description of correlated target states. We describe a successful implementation of the method using completely adaptive overset grids to describe continuum functions, in which spherical subgrids are placed on every atomic center to complement a spherical master grid that describes the behavior at large distances. An accurate method for applying the free-particle Green's function on the grid eliminates the need to operate explicitly with the kinetic energy, enabling a rapidly convergent Arnoldi algorithm for solving linear equations on the grid, and no approximations to exchange operators are made. Results for electron scattering from several polyatomic molecules will be presented. Army Research Office, MURI, WN911NF-14-1-0383 and U. S. DOE DE-SC0012198 (at Texas A&M).
Simplified model to describe the dissociative recombination of linear polyatomic ions of astrophysical interest

NASA Astrophysics Data System (ADS)

Fonseca Dos Santos, Samantha; Douguet, Nicolas; Kokoouline, Viatcheslav; Orel, Ann

2013-05-01

We will present theoretical results on the dissociative recombination (DR) of the linear polyatomic ions HCNH+, HCO+ and N2H+. Besides their astrophysical importance, they also share the characteristic that at low electronic impact energies their DR process happens via the indirect DR mechanism. We apply a general simplified model successfully implemented to treat the DR process of the highly symmetric non-linear molecules H3+, CH3+, H3O+ and NH4+ to calculated cross sections and DR rates for these ions. The model is based on multichannel quantum defect theory and accounts for all the main ingredients of indirect DR. New perspectives on dissociative recombination of HCO+ will also be discussed, including the possible role of HOC+ in storage ring experimental results. This work is supported by the DOE Office of Basic Energy Science and the National Science Foundation, Grant No's PHY-11-60611 and PHY-10-68785.
Electron Interactions with Non-Linear Polyatomic Molecules and Their Radicals

DTIC Science & Technology

1993-12-01

developed which generates SCE quantities from molecular wave functions. This progress was realized in terms of some actual calculations on some molecules...section 4.A describes the basics of the Partial Differential Equation Theory; section 4.B describes the generalization to a finite element...Information Service (NTIS). At NTIS, it will be available to the general public, including foreign nations. This technical report has been reviewed and
Ion mobilities in diatomic gases: measurement versus prediction with non-specular scattering models.

PubMed

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 compact to highly linear, and singly charged tetraalkylammonium cations. It was found that both non-specular, inelastic scattering rules lead to excellent agreement between predictions and experimental mobility measurements (within 5% of each other) and that polarization potentials must be considered to make correct predictions for high-mobility particles/ions. Conversely, traditional specular, elastic scattering models were found to substantially overestimate the mobilities of both types of ions.
Attosecond-recollision-controlled selective fragmentation of polyatomic molecules.

PubMed

Xie, Xinhua; Doblhoff-Dier, Katharina; Roither, Stefan; Schöffler, Markus S; Kartashov, Daniil; Xu, Huailiang; Rathje, Tim; Paulus, Gerhard G; Baltuška, Andrius; Gräfe, Stefanie; Kitzler, Markus

2012-12-14

Control over various fragmentation reactions of a series of polyatomic molecules (acetylene, ethylene, 1,3-butadiene) by the optical waveform of intense few-cycle laser pulses is demonstrated experimentally. We show both experimentally and theoretically that the responsible mechanism is inelastic ionization from inner-valence molecular orbitals by recolliding electron wave packets, whose recollision energy in few-cycle ionizing laser pulses strongly depends on the optical waveform. Our work demonstrates an efficient and selective way of predetermining fragmentation and isomerization reactions in polyatomic molecules on subfemtosecond time scales.
A study of increasing radical density and etch rate using remote plasma generator system

NASA Astrophysics Data System (ADS)

Lee, Jaewon; Kim, Kyunghyun; Cho, Sung-Won; Chung, Chin-Wook

2013-09-01

To improve radical density without changing electron temperature, remote plasma generator (RPG) is applied. Multistep dissociation of the polyatomic molecule was performed using RPG system. RPG is installed to inductively coupled type processing reactor; electrons, positive ions, radicals and polyatomic molecule generated in RPG and they diffused to processing reactor. The processing reactor dissociates the polyatomic molecules with inductively coupled power. The polyatomic molecules are dissociated by the processing reactor that is operated by inductively coupled power. Therefore, the multistep dissociation system generates more radicals than single-step system. The RPG was composed with two cylinder type inductively coupled plasma (ICP) using 400 kHz RF power and nitrogen gas. The processing reactor composed with two turn antenna with 13.56 MHz RF power. Plasma density, electron temperature and radical density were measured with electrical probe and optical methods.
New Ro-Vibrational Kinetic Energy Operators using Polyspherical Coordinates for Polyatomic Molecules

NASA Technical Reports Server (NTRS)

Schwenke, David W.; Kwak, Dochan (Technical Monitor)

2002-01-01

We illustrate how one can easily derive kinetic energy operators for polyatomic molecules using polyspherical coordinates with very general choices for z-axis embeddings arid angles used to specify relative orientations of internal vectors. Computer algebra is not required.
Sympathetic cooling of polyatomic molecules with S-state atoms in a magnetic trap.

PubMed

Tscherbul, T V; Yu, H-G; Dalgarno, A

2011-02-18

We present a rigorous theoretical study of low-temperature collisions of polyatomic molecular radicals with (1)S(0) atoms in the presence of an external magnetic field. Accurate quantum scattering calculations based on ab initio and scaled interaction potentials show that collision-induced spin relaxation of the prototypical organic molecule CH(2)(X(3)B(1)) (methylene) and nine other triatomic radicals in cold (3)He gas occurs at a slow rate, demonstrating that cryogenic buffer-gas cooling and magnetic trapping of these molecules is feasible with current technology. Our calculations further suggest that it may be possible to create ultracold gases of polyatomic molecules by sympathetic cooling with alkaline-earth atoms in a magnetic trap.
Calculations on Isotope Separation by Laser Induced Photodissociation of Polyatomic Molecules. Final Report

DOE R&D Accomplishments Database

Lamb, W. E. Jr.

1978-11-01

This report describes research on the theory of isotope separation produced by the illumination of polyatomic molecules by intense infrared laser radiation. Newton`s equations of motion were integrated for the atoms of the SF{sub 6} molecule including the laser field interaction. The first year`s work has been largely dedicated to obtaining a suitable interatomic potential valid for arbitrary configurations of the seven particles. This potential gives the correct symmetry of the molecule, the equilibrium configuration, the frequencies of the six distinct normal modes of oscillation and the correct (or assumed) value of the total potential energy of the molecule. Other conditions can easily be imposed in order to obtain a more refined potential energy function, for example, by making allowance for anharmonicity data. A suitable expression was also obtained for the interaction energy between a laser field and the polyatomic molecule. The electromagnetic field is treated classically, and it would be easily possible to treat the cases of time dependent pulses, frequency modulation and noise.
Negative ions of polyatomic molecules.

PubMed Central

Christophorou, L G

1980-01-01

In this paper general concepts relating to, and recent advances in, the study of negative ions of polyatomic molecules area discussed with emphasis on halocarbons. The topics dealt with in the paper are as follows: basic electron attachment processes, modes of electron capture by molecules, short-lived transient negative ions, dissociative electron attachment to ground-state molecules and to "hot" molecules (effects of temperature on electron attachment), parent negative ions, effect of density, nature, and state of the medium on electron attachment, electron attachment to electronically excited molecules, the binding of attached electrons to molecules ("electron affinity"), and the basic and the applied significance of negative-ion studies. PMID:7428744
Strong-field ionization of linear molecules by a bicircular laser field: Symmetry considerations

NASA Astrophysics Data System (ADS)

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.
Electrondriven processes in polyatomic molecules

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

McKoy, Vincent

2017-03-20

This project developed and applied scalable computational methods to obtain information about low-energy electron collisions with larger polyatomic molecules. Such collisions are important in modeling radiation damage to living systems, in spark ignition and combustion, and in plasma processing of materials. The focus of the project was to develop efficient methods that could be used to obtain both fundamental scientific insights and data of practical value to applications.
Higher sensitivity secondary ion mass spectrometry of biological molecules for high resolution, chemically specific imaging.

PubMed

McDonnell, Liam A; Heeren, Ron M A; de Lange, Robert P J; Fletcher, Ian W

2006-09-01

To expand the role of high spatial resolution secondary ion mass spectrometry (SIMS) in biological studies, numerous developments have been reported in recent years for enhancing the molecular ion yield of high mass molecules. These include both surface modification, including matrix-enhanced SIMS and metal-assisted SIMS, and polyatomic primary ions. Using rat brain tissue sections and a bismuth primary ion gun able to produce atomic and polyatomic primary ions, we report here how the sensitivity enhancements provided by these developments are additive. Combined surface modification and polyatomic primary ions provided approximately 15.8 times more signal than using atomic primary ions on the raw sample, whereas surface modification and polyatomic primary ions yield approximately 3.8 and approximately 8.4 times more signal. This higher sensitivity is used to generate chemically specific images of higher mass biomolecules using a single molecular ion peak.
Dissipation dynamics of field-free molecular alignment for symmetric-top molecules: Ethane (C2H6)

NASA Astrophysics Data System (ADS)

Zhang, H.; Billard, F.; Yu, X.; Faucher, O.; Lavorel, B.

2018-03-01

The field-free molecular alignment of symmetric-top molecules, ethane, induced by intense non-resonant linearly polarized femtosecond laser pulses is investigated experimentally in the presence of collisional relaxation. The dissipation dynamics of field-free molecular alignment are measured by the balanced detection of ultrafast molecular birefringence of ethane gas samples at high pressures. By separating the molecular alignment into the permanent alignment and the transient alignment, the decay time-constants of both components are quantified at the same pressure. It is observed that the permanent alignment always decays slower compared to the transient alignment within the measured pressure range. This demonstrates that the propensity of molecules to conserve the orientation of angular momentum during collisions, previously observed for linear species, is also applicable to symmetric-top molecules. The results of this work provide valuable information for further theoretical understanding of collisional relaxation within nonlinear polyatomic molecules, which are expected to present interesting and nontrivial features due to an extra rotational degree of freedom.
Measurements of Polyatomic Molecule Formation on an Icy Grain Analog Using Fast Atoms

NASA Technical Reports Server (NTRS)

Chutjian, A.; Madsunkov, S.; Shortt, B. J.; MacAskill, J. A.; Darrach, M. R.

2006-01-01

Carbon dioxide has been produced from the impact of a monoenergetic O(P-3) beam upon a surface cooled to 4.8 K and covered with a CO ice. Using temperature-programmed desorption and mass spectrometer detection, we have detected increasing amounts of CO2 formation with O(P-3) energies of 2, 5, 10, and 14 eV. This is the first measurement of polyatomic molecule formation on a surface with superthermal atoms. The goal of this work is to detect other polyatomic species, such as CH3OH, which can be formed under conditions that simulate the grain temperature, surface coverage, and superthermal atoms present in shock-heated circumstellar and interstellar regions.
Scattering matrix approach to the dissociative recombination of HCO{sup +} and N{sub 2}H{sup +}

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

Fonseca dos Santos, S.; Douguet, N.; Orel, A. E.

We present a theoretical study of the indirect dissociative recombination of linear polyatomic ions at low collisional energies. The approach is based on the computation of the scattering matrix just above the ionization threshold and enables the explicit determination of all diabatic electronic couplings responsible for dissociative recombination. In addition, we use the multi-channel quantum-defect theory to demonstrate the precision of the scattering matrix by reproducing accurately ab initio Rydberg state energies of the neutral molecule. We consider the molecular ions N{sub 2}H{sup +} and HCO{sup +} as benchmark systems of astrophysical interest and improve former theoretical studies, which hadmore » repeatedly produced smaller cross sections than experimentally measured. Specifically, we demonstrate the crucial role of the previously overlooked stretching modes for linear polyatomic ions with large permanent dipole moment. The theoretical cross sections for both ions agree well with experimental data over a wide energy range. Finally, we consider the potential role of the HOC{sup +} isomer in the experimental cross sections of HCO{sup +} at energies below 10 meV.« less
Fit Point-Wise AB Initio Calculation Potential Energies to a Multi-Dimension Long-Range Model

NASA Astrophysics Data System (ADS)

Zhai, Yu; Li, Hui; Le Roy, Robert J.

2016-06-01

A potential energy surface (PES) is a fundamental tool and source of understanding for theoretical spectroscopy and for dynamical simulations. Making correct assignments for high-resolution rovibrational spectra of floppy polyatomic and van der Waals molecules often relies heavily on predictions generated from a high quality ab initio potential energy surface. Moreover, having an effective analytic model to represent such surfaces can be as important as the ab initio results themselves. For the one-dimensional potentials of diatomic molecules, the most successful such model to date is arguably the ``Morse/Long-Range'' (MLR) function developed by R. J. Le Roy and coworkers. It is very flexible, is everywhere differentiable to all orders. It incorporates correct predicted long-range behaviour, extrapolates sensibly at both large and small distances, and two of its defining parameters are always the physically meaningful well depth {D}_e and equilibrium distance r_e. Extensions of this model, called the Multi-Dimension Morse/Long-Range (MD-MLR) function, linear molecule-linear molecule systems and atom-non-linear molecule system. have been applied successfully to atom-plus-linear molecule, linear molecule-linear molecule and atom-non-linear molecule systems. However, there are several technical challenges faced in modelling the interactions of general molecule-molecule systems, such as the absence of radial minima for some relative alignments, difficulties in fitting short-range potential energies, and challenges in determining relative-orientation dependent long-range coefficients. This talk will illustrate some of these challenges and describe our ongoing work in addressing them. Mol. Phys. 105, 663 (2007); J. Chem. Phys. 131, 204309 (2009); Mol. Phys. 109, 435 (2011). Phys. Chem. Chem. Phys. 10, 4128 (2008); J. Chem. Phys. 130, 144305 (2009) J. Chem. Phys. 132, 214309 (2010) J. Chem. Phys. 140, 214309 (2010)
Earle K. Plyler Prize Lecture: The Three Pillars of Ultrafast Molecular Science - Time, Phase, Intensity

NASA Astrophysics Data System (ADS)

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 polyatomic molecules, including high harmonic generation (HHG). We discuss an experimental method, Channel-Resolved Above Threshold Ionization (CRATI), which directly unveils the electronic channels participating in the attosecond molecular strong field ionization response [10]. This work was supported by the National Research Council of Canada and the Natural Sciences & Engineering Research Council.
Discrete Velocity Models for Polyatomic Molecules Without Nonphysical Collision Invariants

NASA Astrophysics Data System (ADS)

Bernhoff, Niclas

2018-05-01

An important aspect of constructing discrete velocity models (DVMs) for the Boltzmann equation is to obtain the right number of collision invariants. Unlike for the Boltzmann equation, for DVMs there can appear extra collision invariants, so called spurious collision invariants, in plus to the physical ones. A DVM with only physical collision invariants, and hence, without spurious ones, is called normal. The construction of such normal DVMs has been studied a lot in the literature for single species, but also for binary mixtures and recently extensively for multicomponent mixtures. In this paper, we address ways of constructing normal DVMs for polyatomic molecules (here represented by that each molecule has an internal energy, to account for non-translational energies, which can change during collisions), under the assumption that the set of allowed internal energies are finite. We present general algorithms for constructing such models, but we also give concrete examples of such constructions. This approach can also be combined with similar constructions of multicomponent mixtures to obtain multicomponent mixtures with polyatomic molecules, which is also briefly outlined. Then also, chemical reactions can be added.

Proposed Molecular Beam Determination of Energy Partition in the Photodissociation of Polyatomic Molecules

DOE R&D Accomplishments Database

Zare, P. N.; Herschbach, D. R.

1964-01-29

Conventional photochemical experiments give no information about the partitioning of energy between translational recoil and internal excitation of the fragment molecules formed in photodissociation of a polyatomic molecule. In a molecular beam experiment, it becomes possible to determine the energy partition from the form of the laboratory angular distribution of one of the photodissociation products. A general kinematic analysis is worked out in detail, and the uncertainty introduced by the finite angular resolution of the apparatus and the velocity spread in the parent beam is examined. The experimental requirements are evaluated for he photolysis of methyl iodide by the 2537 angstrom Hg line.
Theory of attosecond delays in molecular photoionization.

PubMed

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.
Electron Interactions with Non-Linear Polyatomic Molecules and their Radicals and Ions

DTIC Science & Technology

1991-06-01

is the usual antisymmetrization operator to ensure Pauli principle. In the expansion (4.1.2), we have neglected the correlation functions of the (N...Kochem, K M Scheuerlein, K Jung and H Ehrhardt, J. Phys. B19, 3625 (1986). [27]. A Jain, Ph.D. thesis (Queen’s University, Belfast) 1983. [2S]. D M...Winstead and V McLoy, Phys. Rev. A42, 5357 (1990). [52]. R Muiller, K Jung , K H Kochem, W Sohn and H Ehrhardt, J. Phys. B 18, 3971 (1985). [53]. L
Sensitivity and resolution in frequency comb spectroscopy of buffer gas cooled polyatomic molecules

NASA Astrophysics Data System (ADS)

Changala, P. Bryan; Spaun, Ben; Patterson, David; Doyle, John M.; Ye, Jun

2016-12-01

We discuss the use of cavity-enhanced direct frequency comb spectroscopy in the mid-infrared region with buffer gas cooling of polyatomic molecules for high-precision rovibrational absorption spectroscopy. A frequency comb coupled to an optical enhancement cavity allows us to collect high-resolution, broad-bandwidth infrared spectra of translationally and rotationally cold (10-20 K) gas-phase molecules with high absorption sensitivity and fast acquisition times. The design and performance of the combined apparatus are discussed in detail. Recorded rovibrational spectra in the CH stretching region of several organic molecules, including vinyl bromide (CH_2CHBr), adamantane (C_{10}H_{16}), and diamantane (C_{14}H_{20}) demonstrate the resolution and sensitivity of this technique, as well as the intrinsic challenges faced in extending the frontier of high-resolution spectroscopy to large complex molecules.
Rapid-Adiabatic Control of Ro-Vibrational Populations in Polyatomic Molecules

NASA Astrophysics Data System (ADS)

Zak, Emil J.; Yachmenev, Andrey

2017-06-01

We present a simple method for control of ro-vibrational populations in polyatomic molecules in the presence of inhomogeneous electric fields [1]. Cooling and trapping of heavy polar polyatomic molecules has become one of the frontier goals in high-resolution molecular spectroscopy, especially in the context of parity violation measurement in chiral compounds [2]. A key step toward reaching this goal would be development of a robust and efficient protocol for control of populations of ro-vibrational states in polyatomic, often floppy molecules. Here we demonstrate a modification of the stark-chirped rapid-adiabatic-passage technique (SCRAP) [3], designed for achieving high levels of control of ro-vibrational populations over a selected region in space. The new method employs inhomogeneous electric fields to generate space- and time- controlled Stark-shifts of energy levels in molecules. Adiabatic passage between ro-vibrational states is enabled by the pump pulse, which raises the value of the Rabi frequency. This Stark-chirped population transfer can be used in manipulation of population differences between high-field-seeking and low-field-seeking states of molecules in the Stark decelerator [4]. Appropriate timing of voltages on electric rods located along the decelerator combined with a single pump laser renders our method as potentially more efficient than traditional Stark decelerator techniques. Simulations for NH_3 show significant improvement in effectiveness of cooling, with respect to the standard 'moving-potential' method [5]. At the same time a high phase-space acceptance of the molecular packet is maintained. E. J. Zak, A. Yachmenev (submitted). C. Medcraft, R. Wolf, M. Schnell, Angew. Chem. Int. Ed., 53, 43, 11656-11659 (2014) M. Oberst, H. Munch, T. Halfman, PRL 99, 173001 (2007). K. Wohlfart, F. Grätz, F. Filsinger, H. Haak, G. Meijer, J. Küpper, Phys. Rev. A 77, 031404(R) (2008). H. L. Bethlem, F. M. H. Crompvoets, R. T. Jongma, S. Y. T. van de Meerakker, G. Meijer, Phys. Rev. A, 65, 053416 (2002).
Polyad quantum numbers and multiple resonances in anharmonic vibrational studies of polyatomic molecules

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

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.more » 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.« less
Optical Control of Internal Conversion in Pyrazine

NASA Astrophysics Data System (ADS)

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.
Time-resolved photoelectron spectroscopy of polyatomic molecules using 42-nm vacuum ultraviolet laser based on high harmonics generation

NASA Astrophysics Data System (ADS)

Nishitani, Junichi; West, Christopher W.; Higashimura, Chika; Suzuki, Toshinori

2017-09-01

Time-resolved photoelectron spectroscopy (TRPES) of gaseous polyatomic molecules using 266-nm (4.7 eV) pump and 42-nm (29.5 eV) probe pulses is presented. A 1-kHz Ti:sapphire laser with a 35 fs pulse duration is employed to generate high harmonics in Kr gas, and the 19th harmonic (42-nm) was selected using two SiC/Mg mirrors. Clear observation of the ultrafast electronic dephasing in pyrazine and photoisomerization of 1,3-cyclohexadiene demonstrates the feasibility of TRPES with the UV pump and VUV probe pulses under weak excitation conditions in the perturbation regime.
Crossed beam (E--VRT) energy transfer experiment

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

Hertel, I.V.; Hofmann, H.; Rost, K.A.

A molecular crossed beam apparatus which has been developed to perform electronic-to-vibrational, rotational, translational (E--V,R,T) energy transfer studies is described. Its capabilities are illustrated on the basis of a number of energy transfer spectra obtained for collision systems of the type Na*+Mol(..nu..,j) ..-->..Na+Mol (..nu..',j') where Na* represents a laser excited sodium atom and Mol a diatomic or polyatomic molecule. Because of the lack of reliable dynamic theories on quenching processes, statistical approaches such as the ''linearly forced harmonic oscillator'' and ''prior distributions'' have been used to model the experimental spectra. The agreement is found to be satisfactory, so even suchmore » simple statistics may be useful to describe (E--V,R,T) energy transfer processes in collision systems with small molecules.« less
The importance of Rydberg orbitals in dissociative ionization of small hydrocarbon molecules in intense laser fields.

PubMed

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.
A new scale of electronegativity based on electrophilicity index.

PubMed

Noorizadeh, Siamak; Shakerzadeh, Ehsan

2008-04-17

By calculating the energies of neutral and different ionic forms (M2+, M+, M, M-, and M2-) of 32 elements (using B3LYP/6-311++G** level of theory) and taking energy (E) to be a Morse-like function of the number of electrons (N), the electrophilicity values (omega) are calculated for these atoms. The obtained electrophilicities show a good linearity with some commonly used electronegativity scales such as Pauling and Allred-Rochow. Using these electrophilicities, the ionicities of some diatomic molecules are calculated, which are in good agreement with the experimental data. Therefore, these electrophilicities are introduced as a new scale for atomic electronegativity, chi(omega)0. The same procedure is also performed for some simple polyatomic molecules. It is shown that the new scale successfully obeys Sanderson's electronegativity equalization principle and for those molecules which have the same number of atoms, the ratio of the change in electronegativity during the formation of a molecule from its elements to the molecular electronegativity (Delta chi/chi omega) is the same.
Enthalpic parameters of interaction between diglycylglycine and polyatomic alcohols in aqueous solutions

NASA Astrophysics Data System (ADS)

Mezhevoi, I. N.; Badelin, V. G.

2015-12-01

Integral enthalpies of solution Δsol H m of diglycylglycine in aqueous solutions of glycerol, ethylene glycol, and 1,2-propylene glycol are measured via solution calorimetry. The experimental data are used to calculate the standard enthalpies of solution (Δsol H°) and transfer (Δtr H°) of the tripeptide from water to aqueous solutions of polyatomic alcohols. The enthalpic pairwise coefficients h xy of interactions between the tripeptide and polyatomic alcohol molecules are calculated using the McMillan-Mayer solution theory and are found to have positive values. The findings are discussed using the theory of estimating various types of interactions in ternary systems and the effect the structural features of interacting biomolecules have on the thermochemical parameters of diglycylglycine dissolution.
Non-equilibrium effects of diatomic and polyatomic gases on the shock-vortex interaction based on the second-order constitutive model of the Boltzmann-Curtiss equation

NASA Astrophysics Data System (ADS)

Singh, S.; Karchani, A.; Myong, R. S.

2018-01-01

The rotational mode of molecules plays a critical role in the behavior of diatomic and polyatomic gases away from equilibrium. In order to investigate the essence of the non-equilibrium effects, the shock-vortex interaction problem was investigated by employing an explicit modal discontinuous Galerkin method. In particular, the first- and second-order constitutive models for diatomic and polyatomic gases derived rigorously from the Boltzmann-Curtiss kinetic equation were solved in conjunction with the physical conservation laws. As compared with a monatomic gas, the non-equilibrium effects result in a substantial change in flow fields in both macroscale and microscale shock-vortex interactions. Specifically, the computational results showed three major effects of diatomic and polyatomic gases on the shock-vortex interaction: (i) the generation of the third sound waves and additional reflected shock waves with strong and enlarged expansion, (ii) the dominance of viscous vorticity generation, and (iii) an increase in enstrophy with increasing bulk viscosity, related to the rotational mode of gas molecules. Moreover, it was shown that there is a significant discrepancy in flow fields between the microscale and macroscale shock-vortex interactions in diatomic and polyatomic gases. The quadrupolar acoustic wave source structures, which are typically observed in macroscale shock-vortex interactions, were not found in any microscale shock-vortex interactions. The physics of the shock-vortex interaction was also investigated in detail to examine vortex deformation and evolution dynamics over an incident shock wave. A comparative study of first- and second-order constitutive models was also conducted for the enstrophy and dissipation rate. Finally, the study was extended to the shock-vortex pair interaction case to examine the effects of pair interaction on vortex deformation and evolution dynamics.
Recent advances in quantum scattering calculations on polyatomic bimolecular reactions.

PubMed

Fu, Bina; Shan, Xiao; Zhang, Dong H; Clary, David C

2017-12-11

This review surveys quantum scattering calculations on chemical reactions of polyatomic molecules in the gas phase published in the last ten years. These calculations are useful because they provide highly accurate information on the dynamics of chemical reactions which can be compared in detail with experimental results. They also serve as quantum mechanical benchmarks for testing approximate theories which can more readily be applied to more complicated reactions. This review includes theories for calculating quantities such as rate constants which have many important scientific applications.
Molecular extended thermodynamics of rarefied polyatomic gases and wave velocities for increasing number of moments

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

Arima, Takashi, E-mail: tks@stat.nitech.ac.jp; Mentrelli, Andrea, E-mail: andrea.mentrelli@unibo.it; Ruggeri, Tommaso, E-mail: tommaso.ruggeri@unibo.it

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 themore » 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.« less
General features of the dissociative recombination of polyatomic molecules

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

Pratt, S. T.; Jungen, Ch.; Schneider, I. F.

We discuss some aspects of a simple expression for the low-energy dissociative recombination cross section that applies when the recombination process is dominated by the indirect mechanism. In most previous applications, this expression has been applied to capture into vibrationally excited Rydberg states with the assumption that capture is always followed by prompt dissociation. Here we consider the dissociative recombination of larger polyatomic ions and electrons. More specifically, we consider capture into electronically core-excited Rydberg states, and begin to assess its potential importance for larger systems.
General features of the dissociative recombination of polyatomic molecules

DOE PAGES

Pratt, S. T.; Jungen, Ch.; Schneider, I. F.; ...

2015-01-29

We discuss some aspects of a simple expression for the low-energy dissociative recombination cross section that applies when the recombination process is dominated by the indirect mechanism. In most previous applications, this expression has been applied to capture into vibrationally excited Rydberg states with the assumption that capture is always followed by prompt dissociation. Here we consider the dissociative recombination of larger polyatomic ions and electrons. More specifically, we consider capture into electronically core-excited Rydberg states, and begin to assess its potential importance for larger systems.
Simplified model to describe the dissociative recombination of linear polyatomic ions of astrophysical interest

NASA Astrophysics Data System (ADS)

Douguet, N.; Fonseca dos Santos, S.; Kokoouline, V.; Orel, A. E.

2015-01-01

We present results of a theoretical study on dissociative recombination of the HCNH+, HCO+ and N2H+ linear polyatomic ions at low energies using a simple theoretical model. In the present study, the indirect mechanism for recombination proceeds through the capture of the incoming electron in excited vibrational Rydberg states attached to the degenerate transverse modes of the linear ions. The strength of the non-adiabatic coupling responsible for dissociative recombination is determined directly from the near-threshold scattering matrix obtained numerically using the complex Kohn variational method. The final cross sections for the process are compared with available experimental data. It is demonstrated that at low collision energies, the major contribution to the dissociative recombination cross section is due to the indirect mechanism.
Proposal for Laser Cooling of Alkaline Earth Monoalkoxide Free Radicals

NASA Astrophysics Data System (ADS)

Baum, Louis; Kozyryev, Ivan; Matsuda, Kyle; Doyle, John M.

2016-05-01

Cold samples of polyatomic molecules will open new avenues in physics, chemistry, and quantum science. Non-diagonal Franck-Condon factors, technically challenging wavelengths, and the lack of strong electronic transitions inhibit direct laser cooling of nonlinear molecules. We identify a scheme for optical cycling in certain molecules with six or more atoms. Replacing hydrogen in alcohols with an alkaline earth metal (M) leads to alkaline earth monoalkoxide free radicals (MOR), which have favorable properties for laser cooling. M-O bond is very ionic, so the metal orbitals are slightly affected by the nature of R on the ligand. Diagonal Franck-Condon factors, laser accessible transitions, and a small hyperfine structure make MOR molecules suitable for laser cooling. We explore a scheme for optical cycling on the A - X transition of SrOCH3 . Molecules lost to dark vibrational states will be repumped on the B - X transition. Extension to larger species is possible through expansion of the R group since transitions involve the promotion of the metal-centered nonbonding valence electron. We will detail our estimations of the Franck-Condon factors, simulations of the cooling process and describe progress towards the Doppler cooling of MOR polyatomics.
An exact variational method to calculate rovibrational spectra of polyatomic molecules with large amplitude motion

NASA Astrophysics Data System (ADS)

Yu, Hua-Gen

2016-08-01

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 CH4 and H2CO are given, together with a comparison with previous results.

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

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

Yu, Hua-Gen, E-mail: hgy@bnl.gov

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 amore » 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.« less
Correlation between molecular secondary ion yield and cluster ion sputtering for samples with different stopping powers

NASA Astrophysics Data System (ADS)

Heile, A.; Muhmann, C.; Lipinsky, D.; Arlinghaus, H. F.

2012-07-01

In static SIMS, the secondary ion yield, defined as detected ions per primary ion, can be increased by altering several primary ion parameters. For many years, no quantitative predictions could be made for the secondary ion yield enhancement of molecular ions. For thick samples of organic compounds, a power dependency of the secondary ion yield on the sputtering yield was shown. For this article, samples with thick molecular layers and (sub-)monolayers composed of various molecules were prepared on inorganic substrates such as silicon, silver, and gold, and subsequently analyzed. For primary ion bombardment, monoatomic (Ne+, Ar+, Ga+, Kr+, Xe+, Bi+) as well as polyatomic (Bin+, Bin++) primary ions were used within an energy range of 10-50 keV. The power dependency was found to hold true for the different samples; however, the exponent decreased with increasing stopping power. Based on these findings, a rule of thumb is proposed for the prediction of the lower limit of the secondary ion yield enhancement as a function of the primary ion species. Additionally, effects caused by the variation of the energy deposition are discussed, including the degree of molecular fragmentation and the non-linear increase of the secondary ion yield when polyatomic primary ions are used.
A systematic and feasible method for computing nuclear contributions to electrical properties of polyatomic molecules

NASA Astrophysics Data System (ADS)

Luis, Josep M.; Duran, Miquel; Andrés, José L.

1997-08-01

An analytic method to evaluate nuclear contributions to electrical properties of polyatomic molecules is presented. Such contributions control changes induced by an electric field on equilibrium geometry (nuclear relaxation contribution) and vibrational motion (vibrational contribution) of a molecular system. Expressions to compute the nuclear contributions have been derived from a power series expansion of the potential energy. These contributions to the electrical properties are given in terms of energy derivatives with respect to normal coordinates, electric field intensity or both. Only one calculation of such derivatives at the field-free equilibrium geometry is required. To show the useful efficiency of the analytical evaluation of electrical properties (the so-called AEEP method), results for calculations on water and pyridine at the SCF/TZ2P and the MP2/TZ2P levels of theory are reported. The results obtained are compared with previous theoretical calculations and with experimental values.
Polyatomic molecular Dirac-Hartree-Fock calculations with Gaussian basis sets

NASA Technical Reports Server (NTRS)

Dyall, Kenneth G.; Faegri, Knut, Jr.; Taylor, Peter R.

1990-01-01

Numerical methods have been used successfully in atomic Dirac-Hartree-Fock (DHF) calculations for many years. Some DHF calculations using numerical methods have been done on diatomic molecules, but while these serve a useful purpose for calibration, the computational effort in extending this approach to polyatomic molecules is prohibitive. An alternative more in line with traditional quantum chemistry is to use an analytical basis set expansion of the wave function. This approach fell into disrepute in the early 1980's due to problems with variational collapse and intruder states, but has recently been put on firm theoretical foundations. In particular, the problems of variational collapse are well understood, and prescriptions for avoiding the most serious failures have been developed. Consequently, it is now possible to develop reliable molecular programs using basis set methods. This paper describes such a program and reports results of test calculations to demonstrate the convergence and stability of the method.
High Resolution Studies of the Origins of Polyatomic Ions in Inductively Coupled Plasma-Mass Spectrometry

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

Ferguson, Jill Wisnewski

2006-01-01

The inductively coupled plasma (ICP) is an atmospheric pressure ionization source. Traditionally, the plasma is sampled via a sampler cone. A supersonic jet develops behind the sampler, and this region is pumped down to a pressure of approximately one Torr. A skimmer cone is located inside this zone of silence to transmit ions into the mass spectrometer. The position of the sampler and skimmer cones relative to the initial radiation and normal analytical zones of the plasma is key to optimizing the useful analytical signal [1]. The ICP both atomizes and ionizes the sample. Polyatomic ions form through ion-molecule interactionsmore » either in the ICP or during ion extraction [l]. Common polyatomic ions that inhibit analysis include metal oxides (MO +), adducts with argon, the gas most commonly used to make up the plasma, and hydride species. While high resolution devices can separate many analytes from common interferences, this is done at great cost in ion transmission efficiency--a loss of 99% when using high versus low resolution on the same instrument [2]. Simple quadrupole devices, which make up the bulk of ICP-MS instruments in existence, do not present this option. Therefore, if the source of polyatomic interferences can be determined and then manipulated, this could potentially improve the figures of merit on all ICP-MS devices, not just the high resolution devices often utilized to study polyatomic interferences.« less
Studies of electron-polyatomic-molecule collisions Applications to e-CH4

NASA Technical Reports Server (NTRS)

Lima, M. A. P.; Gibson, T. L.; Mckoy, V.; Huo, W. M.

1985-01-01

The first application of the Schwinger multichannel formulation to low-energy electron collisions with a nonlinear polyatomic target is reported. Integral and differential cross sections are obtained for e-CH4 collisions from 3 to 20 eV at the static-plus-exchange interaction level. In these studies, the exchange potential is directly evaluated and not approximated by local models. An interesting feature of the small-angle differential cross section is ascribed to polarization effects and not reproduced at the static-plus-exchange level. These differential cross sections are found to be in reasonable agreement with existing measurements at 7.5 eV and higher energies.
Intramolecular energy transfer and the driving mechanisms for large-amplitude collective motions of clusters

NASA Astrophysics Data System (ADS)

Yanao, Tomohiro; Koon, Wang Sang; Marsden, Jerrold E.

2009-04-01

This paper uncovers novel and specific dynamical mechanisms that initiate large-amplitude collective motions in polyatomic molecules. These mechanisms are understood in terms of intramolecular energy transfer between modes and driving forces. Structural transition dynamics of a six-atom cluster between a symmetric and an elongated isomer is highlighted as an illustrative example of what is a general message. First, we introduce a general method of hyperspherical mode analysis to analyze the energy transfer among internal modes of polyatomic molecules. In this method, the (3n-6) internal modes of an n-atom molecule are classified generally into three coarse level gyration-radius modes, three fine level twisting modes, and (3n-12) fine level shearing modes. We show that a large amount of kinetic energy flows into the gyration-radius modes when the cluster undergoes structural transitions by changing its mass distribution. Based on this fact, we construct a reactive mode as a linear combination of the three gyration-radius modes. It is shown that before the reactive mode acquires a large amount of kinetic energy, activation or inactivation of the twisting modes, depending on the geometry of the isomer, plays crucial roles for the onset of a structural transition. Specifically, in a symmetric isomer with a spherical mass distribution, activation of specific twisting modes drives the structural transition into an elongated isomer by inducing a strong internal centrifugal force, which has the effect of elongating the mass distribution of the system. On the other hand, in an elongated isomer, inactivation of specific twisting modes initiates the structural transition into a symmetric isomer with lower potential energy by suppressing the elongation effect of the internal centrifugal force and making the effects of the potential force dominant. This driving mechanism for reactions as well as the present method of hyperspherical mode analysis should be widely applicable to molecular reactions in which a system changes its overall mass distribution in a significant way.
Line Mixing in Parallel and Perpendicular Bands of CO2: A Further Test of the Refined Robert-Bonamy Formalism

NASA Technical Reports Server (NTRS)

Boulet, C.; Ma, Qiancheng; Tipping, R. H.

2015-01-01

Starting from the refined Robert-Bonamy formalism [Q. Ma, C. Boulet, and R. H. Tipping, J. Chem. Phys. 139, 034305 (2013)], we propose here an extension of line mixing studies to infrared absorptions of linear polyatomic molecules having stretching and bending modes. The present formalism does not neglect the internal degrees of freedom of the perturbing molecules, contrary to the energy corrected sudden (ECS) modeling, and enables one to calculate the whole relaxation matrix starting from the potential energy surface. Meanwhile, similar to the ECS modeling, the present formalism properly accounts for roles played by all the internal angular momenta in the coupling process, including the vibrational angular momentum. The formalism has been applied to the important case of CO2 broadened by N2. Applications to two kinds of vibrational bands (sigma yields sigma and sigma yields pi) have shown that the present results are in good agreement with both experimental data and results derived from the ECS model.
Vibrational Energy in Molecules and Nanoparticles: Applications to Energetic Materials

DTIC Science & Technology

2009-01-30

of vibrational energy in a polyatomic molecule, nitromethane . Work on water and amino acids partially supported by AFOSR are developmental in nature...have characterized the surface vibrations of HMX explosive and their interaction with polymer binders. We have introduced a major improvement in SFG...Vibrational energy in nitromethane and benzene E. Time resolved spectroscopy of chemistry in flash-heated nanoenergetic materials F. Complete
Detection of anions by normal Raman spectroscopy and surface-enhanced Raman spectroscopy of cationic-coated substrates.

PubMed

Mosier-Boss, P A; Lieberman, S H

2003-09-01

The use of normal Raman spectroscopy and surface-enhanced Raman spectroscopy (SERS) of cationic-coated silver and gold substrates to detect polyatomic anions in aqueous environments is examined. For normal Raman spectroscopy, using near-infrared excitation, linear concentration responses were observed. Detection limits varied from 84 ppm for perchlorate to 2600 ppm for phosphate. In general, detection limits in the ppb to ppm concentration range for the polyatomic anions were achieved using cationic-coated SERS substrates. Adsorption of the polyatomic anions on the cationic-coated SERS substrates was described by a Frumkin isotherm. The SERS technique could not be used to detect dichromate, as this anion reacted with the coatings to form thiol esters. A competitive complexation method was used to evaluate the interaction of chloride ion with the cationic coatings. Hydrogen bonding and pi-pi interactions play significant roles in the selectivity of the cationic coatings.
Extension of the MIRS computer package for the modeling of molecular spectra: From effective to full ab initio ro-vibrational Hamiltonians in irreducible tensor form

NASA Astrophysics Data System (ADS)

Nikitin, A. V.; Rey, M.; Champion, J. P.; Tyuterev, Vl. G.

2012-07-01

The MIRS software for the modeling of ro-vibrational spectra of polyatomic molecules was considerably extended and improved. The original version [Nikitin AV, Champion JP, Tyuterev VlG. The MIRS computer package for modeling the rovibrational spectra of polyatomic molecules. J Quant Spectrosc Radiat Transf 2003;82:239-49.] was especially designed for separate or simultaneous treatments of complex band systems of polyatomic molecules. It was set up in the frame of effective polyad models by using algorithms based on advanced group theory algebra to take full account of symmetry properties. It has been successfully used for predictions and data fitting (positions and intensities) of numerous spectra of symmetric and spherical top molecules within the vibration extrapolation scheme. The new version offers more advanced possibilities for spectra calculations and modeling by getting rid of several previous limitations particularly for the size of polyads and the number of tensors involved. It allows dealing with overlapping polyads and includes more efficient and faster algorithms for the calculation of coefficients related to molecular symmetry properties (6C, 9C and 12C symbols for C3v, Td, and Oh point groups) and for better convergence of least-square-fit iterations as well. The new version is not limited to polyad effective models. It also allows direct predictions using full ab initio ro-vibrational normal mode Hamiltonians converted into the irreducible tensor form. Illustrative examples on CH3D, CH4, CH3Cl, CH3F and PH3 are reported reflecting the present status of data available. It is written in C++ for standard PC computer operating under Windows. The full package including on-line documentation and recent data are freely available at http://www.iao.ru/mirs/mirs.htm or http://xeon.univ-reims.fr/Mirs/ or http://icb.u-bourgogne.fr/OMR/SMA/SHTDS/MIRS.html and as supplementary data from the online version of the article.
Molecular-beam Studies of Primary Photochemical Processes

DOE R&D Accomplishments Database

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.
Matrix-enhanced secondary ion mass spectrometry: The Alchemist's solution?

NASA Astrophysics Data System (ADS)

Delcorte, Arnaud

2006-07-01

Because of the requirements of large molecule characterization and high-lateral resolution SIMS imaging, the possibility of improving molecular ion yields by the use of specific sample preparation procedures has recently generated a renewed interest in the static SIMS community. In comparison with polyatomic projectiles, however, signal enhancement by a matrix might appear to some as the alchemist's versus the scientist's solution to the current problems of organic SIMS. In this contribution, I would like to discuss critically the pros and cons of matrix-enhanced SIMS procedures, in the new framework that includes polyatomic ion bombardment. This discussion is based on a short review of the experimental and theoretical developments achieved in the last decade with respect to the three following approaches: (i) blending the analyte with a low-molecular weight organic matrix (MALDI-type preparation procedure); (ii) mixing alkali/noble metal salts with the analyte; (iii) evaporating a noble metal layer on the analyte sample surface (organic molecules, polymers).
Dual chain perturbation theory: A new equation of state for polyatomic molecules

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

Marshall, Bennett D., E-mail: bennett.d.marshall@exxonmobil.com

In the development of equations of state for polyatomic molecules, thermodynamic perturbation theory (TPT) is widely used to calculate the change in free energy due to chain formation. TPT is a simplification of a more general and exact multi-density cluster expansion for associating fluids. In TPT, all contributions to the cluster expansion which contain chain–chain interactions are neglected. That is, all inter-chain interactions are treated at the reference fluid level. This allows for the summation of the cluster theory in terms of reference system correlation functions only. The resulting theory has been shown to be accurate and has been widelymore » employed as the basis of many engineering equations of state. While highly successful, TPT has many handicaps which result from the neglect of chain–chain contributions. The subject of this document is to move beyond the limitations of TPT and include chain–chain contributions to the equation of state.« less
Multi-layer Lanczos iteration approach to calculations of vibrational energies and dipole transition intensities for polyatomic molecules

DOE PAGES

Yu, Hua-Gen

2015-01-28

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 applicationmore » is illustrated by calculating the infrared vibrational dipole transition spectrum of CH₄ 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.« less
Femtosecond response of polyatomic molecules to ultra-intense hard X-rays.

PubMed

Rudenko, A; Inhester, L; Hanasaki, K; Li, X; Robatjazi, S J; Erk, B; Boll, R; Toyota, K; Hao, Y; Vendrell, O; Bomme, C; Savelyev, E; Rudek, B; Foucar, L; Southworth, S H; Lehmann, C S; Kraessig, B; Marchenko, T; Simon, M; Ueda, K; Ferguson, K R; Bucher, M; Gorkhover, T; Carron, S; Alonso-Mori, R; Koglin, J E; Correa, J; Williams, G J; Boutet, S; Young, L; Bostedt, C; Son, S-K; Santra, R; Rolles, D

2017-06-01

X-ray free-electron lasers enable the investigation of the structure and dynamics of diverse systems, including atoms, molecules, nanocrystals and single bioparticles, under extreme conditions. Many imaging applications that target biological systems and complex materials use hard X-ray pulses with extremely high peak intensities (exceeding 10 20 watts per square centimetre). However, fundamental investigations have focused mainly on the individual response of atoms and small molecules using soft X-rays with much lower intensities. Studies with intense X-ray pulses have shown that irradiated atoms reach a very high degree of ionization, owing to multiphoton absorption, which in a heteronuclear molecular system occurs predominantly locally on a heavy atom (provided that the absorption cross-section of the heavy atom is considerably larger than those of its neighbours) and is followed by efficient redistribution of the induced charge. In serial femtosecond crystallography of biological objects-an application of X-ray free-electron lasers that greatly enhances our ability to determine protein structure-the ionization of heavy atoms increases the local radiation damage that is seen in the diffraction patterns of these objects and has been suggested as a way of phasing the diffraction data. On the basis of experiments using either soft or less-intense hard X-rays, it is thought that the induced charge and associated radiation damage of atoms in polyatomic molecules can be inferred from the charge that is induced in an isolated atom under otherwise comparable irradiation conditions. Here we show that the femtosecond response of small polyatomic molecules that contain one heavy atom to ultra-intense (with intensities approaching 10 20 watts per square centimetre), hard (with photon energies of 8.3 kiloelectronvolts) X-ray pulses is qualitatively different: our experimental and modelling results establish that, under these conditions, the ionization of a molecule is considerably enhanced compared to that of an individual heavy atom with the same absorption cross-section. This enhancement is driven by ultrafast charge transfer within the molecule, which refills the core holes that are created in the heavy atom, providing further targets for inner-shell ionization and resulting in the emission of more than 50 electrons during the X-ray pulse. Our results demonstrate that efficient modelling of X-ray-driven processes in complex systems at ultrahigh intensities is feasible.
Femtosecond response of polyatomic molecules to ultra-intense hard X-rays

DOE PAGES

Rudenko, A.; Inhester, L.; Hanasaki, K.; ...

2017-05-31

We report x-ray free-electron lasers enable the investigation of the structure and dynamics of diverse systems, including atoms, molecules, nanocrystals and single bioparticles, under extreme conditions. Many imaging applications that target biological systems and complex materials use hard X-ray pulses with extremely high peak intensities (exceeding 10 20 watts per square centimetre). However, fundamental investigations have focused mainly on the individual response of atoms and small molecules using soft X-rays with much lower intensities. Studies with intense X-ray pulses have shown that irradiated atoms reach a very high degree of ionization, owing to multiphoton absorption, which in a heteronuclear molecularmore » system occurs predominantly locally on a heavy atom (provided that the absorption cross-section of the heavy atom is considerably larger than those of its neighbours) and is followed by efficient redistribution of the induced charge. In serial femtosecond crystallography of biological objects—an application of X-ray free-electron lasers that greatly enhances our ability to determine protein structure—the ionization of heavy atoms increases the local radiation damage that is seen in the diffraction patterns of these objects and has been suggested as a way of phasing the diffraction data. On the basis of experiments using either soft or less-intense hard X-rays, it is thought that the induced charge and associated radiation damage of atoms in polyatomic molecules can be inferred from the charge that is induced in an isolated atom under otherwise comparable irradiation conditions. Here we show that the femtosecond response of small polyatomic molecules that contain one heavy atom to ultra-intense (with intensities approaching 10 20 watts per square centimetre), hard (with photon energies of 8.3 kiloelectronvolts) X-ray pulses is qualitatively different: our experimental and modelling results establish that, under these conditions, the ionization of a molecule is considerably enhanced compared to that of an individual heavy atom with the same absorption cross-section. This enhancement is driven by ultrafast charge transfer within the molecule, which refills the core holes that are created in the heavy atom, providing further targets for inner-shell ionization and resulting in the emission of more than 50 electrons during the X-ray pulse. Fnally, our results demonstrate that efficient modelling of X-ray-driven processes in complex systems at ultrahigh intensities is feasible.« less
Femtosecond response of polyatomic molecules to ultra-intense hard X-rays

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

Rudenko, A.; Inhester, L.; Hanasaki, K.

We report x-ray free-electron lasers enable the investigation of the structure and dynamics of diverse systems, including atoms, molecules, nanocrystals and single bioparticles, under extreme conditions. Many imaging applications that target biological systems and complex materials use hard X-ray pulses with extremely high peak intensities (exceeding 10 20 watts per square centimetre). However, fundamental investigations have focused mainly on the individual response of atoms and small molecules using soft X-rays with much lower intensities. Studies with intense X-ray pulses have shown that irradiated atoms reach a very high degree of ionization, owing to multiphoton absorption, which in a heteronuclear molecularmore » system occurs predominantly locally on a heavy atom (provided that the absorption cross-section of the heavy atom is considerably larger than those of its neighbours) and is followed by efficient redistribution of the induced charge. In serial femtosecond crystallography of biological objects—an application of X-ray free-electron lasers that greatly enhances our ability to determine protein structure—the ionization of heavy atoms increases the local radiation damage that is seen in the diffraction patterns of these objects and has been suggested as a way of phasing the diffraction data. On the basis of experiments using either soft or less-intense hard X-rays, it is thought that the induced charge and associated radiation damage of atoms in polyatomic molecules can be inferred from the charge that is induced in an isolated atom under otherwise comparable irradiation conditions. Here we show that the femtosecond response of small polyatomic molecules that contain one heavy atom to ultra-intense (with intensities approaching 10 20 watts per square centimetre), hard (with photon energies of 8.3 kiloelectronvolts) X-ray pulses is qualitatively different: our experimental and modelling results establish that, under these conditions, the ionization of a molecule is considerably enhanced compared to that of an individual heavy atom with the same absorption cross-section. This enhancement is driven by ultrafast charge transfer within the molecule, which refills the core holes that are created in the heavy atom, providing further targets for inner-shell ionization and resulting in the emission of more than 50 electrons during the X-ray pulse. Fnally, our results demonstrate that efficient modelling of X-ray-driven processes in complex systems at ultrahigh intensities is feasible.« less
The role of axis embedding on rigid rotor decomposition analysis of variational rovibrational wave functions.

PubMed

Szidarovszky, Tamás; Fábri, Csaba; Császár, Attila G

2012-05-07

Approximate rotational characterization of variational rovibrational wave functions via the rigid rotor decomposition (RRD) protocol is developed for Hamiltonians based on arbitrary sets of internal coordinates and axis embeddings. An efficient and general procedure is given that allows employing the Eckart embedding with arbitrary polyatomic Hamiltonians through a fully numerical approach. RRD tables formed by projecting rotational-vibrational wave functions into products of rigid-rotor basis functions and previously determined vibrational eigenstates yield rigid-rotor labels for rovibrational eigenstates by selecting the largest overlap. Embedding-dependent RRD analyses are performed, up to high energies and rotational excitations, for the H(2) (16)O isotopologue of the water molecule. Irrespective of the embedding chosen, the RRD procedure proves effective in providing unambiguous rotational assignments at low energies and J values. Rotational labeling of rovibrational states of H(2) (16)O proves to be increasingly difficult beyond about 10,000 cm(-1), close to the barrier to linearity of the water molecule. For medium energies and excitations the Eckart embedding yields the largest RRD coefficients, thus providing the largest number of unambiguous rotational labels.
HIGH RESOLUTION SPECTROSCOPY IN THE GAS PHASE: Even Large Molecules Have Well-Defined Shapes

NASA Astrophysics Data System (ADS)

Pratt, David W.

1998-10-01

A review of recent high-resolution microwave, infrared, and optical spectroscopy experiments demonstrates that remarkable progress has been made in the past 20 years in determining the equilibrium geometries of large polyatomic molecules and their clusters in the gas phase, and how these geometries change when the photon is absorbed. A special focus is on the dynamical information that can be obtained from such studies, particularly of electronically excited states.

Rayleigh-Brillouin light scattering spectroscopy of nitrous oxide (N2O)

NASA Astrophysics Data System (ADS)

Wang, Y.; Liang, K.; van de Water, W.; Marques, W.; Ubachs, W.

2018-02-01

High signal-to-noise and high-resolution light scattering spectra are measured for nitrous oxide (N2O) gas at an incident wavelength of 403.00 nm, at 90° scattering, at room temperature and at gas pressures in the range 0.5 - 4 bar. The resulting Rayleigh-Brillouin light scattering spectra are compared to a number of models describing in an approximate manner the collisional dynamics and energy transfer in this gaseous medium of this polyatomic molecular species. The Tenti-S6 model, based on macroscopic gas transport coefficients, reproduces the scattering profiles in the entire pressure range at less than 2% deviation at a similar level as does the alternative kinetic Grad's 6-moment model, which is based on the internal collisional relaxation as a decisive parameter. A hydrodynamic model fails to reproduce experimental spectra for the low pressures of 0.5-1 bar, but yields very good agreement ( < 1%) in the pressure range 2 - 4 bar. While these three models have a different physical basis the internal molecular relaxation derived can for all three be described in terms of a bulk viscosity of ηb ∼(6 ± 2) ×10-5 Pa · s. A 'rough-sphere' model, previously shown to be effective to describe light scattering in SF6 gas, is not found to be suitable, likely in view of the non-sphericity and asymmetry of the N-N-O structured linear polyatomic molecule.
Time-Dependent Wave Packet Dynamics Calculations of Cross Sections for Ultracold Scattering of Molecules

NASA Astrophysics Data System (ADS)

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.
Simulating electric field interactions with polar molecules using spectroscopic databases

NASA Astrophysics Data System (ADS)

Owens, Alec; Zak, Emil J.; Chubb, Katy L.; Yurchenko, Sergei N.; Tennyson, Jonathan; Yachmenev, Andrey

2017-03-01

Ro-vibrational Stark-associated phenomena of small polyatomic molecules are modelled using extensive spectroscopic data generated as part of the ExoMol project. The external field Hamiltonian is built from the computed ro-vibrational line list of the molecule in question. The Hamiltonian we propose is general and suitable for any polar molecule in the presence of an electric field. By exploiting precomputed data, the often prohibitively expensive computations associated with high accuracy simulations of molecule-field interactions are avoided. Applications to strong terahertz field-induced ro-vibrational dynamics of PH3 and NH3, and spontaneous emission data for optoelectrical Sisyphus cooling of H2CO and CH3Cl are discussed.
Time-Dependent Wave Packet Dynamics Calculations of Cross Sections for Ultracold Scattering of Molecules.

PubMed

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

2018-04-06

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.
Stabilizing potentials in bound state analytic continuation methods for electronic resonances in polyatomic molecules

DOE PAGES

White, Alec F.; Head-Gordon, Martin; McCurdy, C. William

2017-01-30

The computation of Siegert energies by analytic continuation of bound state energies has recently been applied to shape resonances in polyatomic molecules by several authors. Here, we critically evaluate a recently proposed analytic continuation method based on low order (type III) Padé approximants as well as an analytic continuation method based on high order (type II) Padé approximants. We compare three classes of stabilizing potentials: Coulomb potentials, Gaussian potentials, and attenuated Coulomb potentials. These methods are applied to a model potential where the correct answer is known exactly and to the 2Π g shape resonance of N 2 - whichmore » has been studied extensively by other methods. Both the choice of stabilizing potential and method of analytic continuation prove to be important to the accuracy of the results. We then conclude that an attenuated Coulomb potential is the most effective of the three for bound state analytic continuation methods. With the proper potential, such methods show promise for algorithmic determination of the positions and widths of molecular shape resonances.« less
Variational treatment of electron-polyatomic-molecule scattering calculations using adaptive overset grids

NASA Astrophysics Data System (ADS)

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.
Stabilizing potentials in bound state analytic continuation methods for electronic resonances in polyatomic molecules

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

White, Alec F.; Head-Gordon, Martin; McCurdy, C. William

The computation of Siegert energies by analytic continuation of bound state energies has recently been applied to shape resonances in polyatomic molecules by several authors. Here, we critically evaluate a recently proposed analytic continuation method based on low order (type III) Padé approximants as well as an analytic continuation method based on high order (type II) Padé approximants. We compare three classes of stabilizing potentials: Coulomb potentials, Gaussian potentials, and attenuated Coulomb potentials. These methods are applied to a model potential where the correct answer is known exactly and to the 2Π g shape resonance of N 2 - whichmore » has been studied extensively by other methods. Both the choice of stabilizing potential and method of analytic continuation prove to be important to the accuracy of the results. We then conclude that an attenuated Coulomb potential is the most effective of the three for bound state analytic continuation methods. With the proper potential, such methods show promise for algorithmic determination of the positions and widths of molecular shape resonances.« less
DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhai, Liangjun; Zheng, Yujun, E-mail: yzheng@sdu.edu.cn

In the present study, the dynamical behaviors of tripartite entanglement of vibrations in triatomic molecules are studied based on the Lie algebraic models of molecules. The dynamical behaviors of tripartite entanglement of the local mode molecule H{sub 2}O and normal mode molecule NO{sub 2} are comparatively studied for different initial states by employing the general concurrence. Our results show that the dynamics of tripartite entanglement are relied on the dynamics of intramolecular energy distribution. The local mode molecule is more suitable to construct the tripartite entangled states. Also, the greater degree of tripartite entanglement can be obtained if the stretchingmore » vibration is first excited. These results shed new light on the understanding of quantum multipartite entanglement of vibrations in the polyatomic molecules.« less
The parity-adapted basis set in the formulation of the photofragment angular momentum polarization problem: The role of the Coriolis interaction

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

Shternin, Peter S.; Vasyutinskii, Oleg S.

We present a theoretical framework for calculating the recoil-angle dependence of the photofragment angular momentum polarization taking into account both radial and Coriolis nonadiabatic interactions in the diatomic/linear photodissociating molecules. The parity-adapted representation of the total molecular wave function has been used throughout the paper. The obtained full quantum-mechanical expressions for the photofragment state multipoles have been simplified by using the semiclassical approximation in the high-J limit and then analyzed for the cases of direct photodissociation and slow predissociation in terms of the anisotropy parameters. In both cases, each anisotropy parameter can be presented as a linear combination of themore » generalized dynamical functions f{sub K}(q,q{sup '},q-tilde,q-tilde{sup '}) of the rank K representing contribution from different dissociation mechanisms including possible radial and Coriolis nonadiabatic transitions, coherent effects, and the rotation of the recoil axis. In the absence of the Coriolis interactions, the obtained results are equivalent to the earlier published ones. The angle-recoil dependence of the photofragment state multipoles for an arbitrary photolysis reaction is derived. As shown, the polarization of the photofragments in the photolysis of a diatomic or a polyatomic molecule can be described in terms of the anisotropy parameters irrespective of the photodissociation mechanism.« less
Evaporation of Lennard-Jones fluids.

PubMed

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.
Interstellar H3+

PubMed Central

Oka, Takeshi

2006-01-01

Protonated molecular hydrogen, H3+, is the simplest polyatomic molecule. It is the most abundantly produced interstellar molecule, next only to H2, although its steady state concentration is low because of its extremely high chemical reactivity. H3+ is a strong acid (proton donor) and initiates chains of ion-molecule reactions in interstellar space thus leading to formation of complex molecules. Here, I summarize the understandings on this fundamental species in interstellar space obtained from our infrared observations since its discovery in 1996 and discuss the recent observations and analyses of H3+ in the Central Molecular Zone near the Galatic center that led to a revelation of a vast amount of warm and diffuse gas existing in the region. PMID:16894171
Potential energy surfaces and reaction dynamics of polyatomic molecules

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

Chang, Yan-Tyng

A simple empirical valence bond (EVB) model approach is suggested for constructing global potential energy surfaces for reactions of polyatomic molecular systems. This approach produces smooth and continuous potential surfaces which can be directly utilized in a dynamical study. Two types of reactions are of special interest, the unimolecular dissociation and the unimolecular isomerization. For the first type, the molecular dissociation dynamics of formaldehyde on the ground electronic surface is investigated through classical trajectory calculations on EVB surfaces. The product state distributions and vector correlations obtained from this study suggest very similar behaviors seen in the experiments. The intramolecular hydrogenmore » atom transfer in the formic acid dimer is an example of the isomerization reaction. High level ab initio quantum chemistry calculations are performed to obtain optimized equilibrium and transition state dimer geometries and also the harmonic frequencies.« less
Ultrafast electron dynamics in phenylalanine initiated by attosecond pulses.

PubMed

Calegari, F; Ayuso, D; Trabattoni, A; Belshaw, L; De Camillis, S; Anumula, S; Frassetto, F; Poletto, L; Palacios, A; Decleva, P; Greenwood, J B; Martín, F; Nisoli, M

2014-10-17

In the past decade, attosecond technology has opened up the investigation of ultrafast electronic processes in atoms, simple molecules, and solids. Here, we report the application of isolated attosecond pulses to prompt ionization of the amino acid phenylalanine and the subsequent detection of ultrafast dynamics on a sub-4.5-femtosecond temporal scale, which is shorter than the vibrational response of the molecule. The ability to initiate and observe such electronic dynamics in polyatomic molecules represents a crucial step forward in attosecond science, which is progressively moving toward the investigation of more and more complex systems. Copyright © 2014, American Association for the Advancement of Science.
ITFITS model for vibration--translation energy partitioning in atom-- polyatomic molecule collisions

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

Shobatake, K.; Rice, S.A.; Lee, Y.T.

1973-09-01

A model for vibration-translation energy partitioning in the collinear collision of an atom and an axially symmetric polyatonaic molecule is proposed. The model is based on an extension of the ideas of Mahan and Heidrich, Wilson, and Rapp. Comparison of energy transfers computed from classical trajesctory calculations and the model proposed indicate good agreement when the mass of the free atom is small relative to the mass of the bound atom it strikes. The agreement is less satisfactory when that mass ratio becomes large. (auth)
Metal atom oxidation laser

DOEpatents

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

1975-10-28

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.
Visualization of Potential Energy Function Using an Isoenergy Approach and 3D Prototyping

ERIC Educational Resources Information Center

Teplukhin, Alexander; Babikov, Dmitri

2015-01-01

In our three-dimensional world, one can plot, see, and comprehend a function of two variables at most, V(x,y). One cannot plot a function of three or more variables. For this reason, visualization of the potential energy function in its full dimensionality is impossible even for the smallest polyatomic molecules, such as triatomics. This creates…
Hydrated proton and hydroxide charge transfer at the liquid/vapor interface of water

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

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

2015-07-28

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

NASA Astrophysics Data System (ADS)

de Clercq, Ludwig E.; Botha, Lourens R.; Rohwer, Erich G.; Uys, Hermann; Du Plessis, Anton

2011-03-01

Simulating coherent control with femtosecond pulses on a polyatomic molecule with anharmonic splitting was demonstrated. The simulation mimicked pulse shaping of a Spatial Light Modulator (SLM) and the interaction was described with the Von Neumann equation. A transform limited pulse with a fluence of 600 J/m2 produced 18% of the population in an arbitrarily chosen upper vibrational state, n =2. Phase only and amplitude only shaped pulse produced optimum values of 60% and 40% respectively, of the population in the vibrational state, n=2, after interaction with the ultra short pulse. The combination of phase and amplitude shaping produced the best results, 80% of the population was in the targeted vibrational state, n=2, after interaction. These simulations were carried out with all the population initially in the ground vibrational level. It was found that even at room temperatures (300 Kelvin) that the population in the selected level is comparable with the case where all population is initially in the ground vibrational state. With a 10% noise added to the amplitude and phase masks, selective excitation of the targeted vibrational state is still possible.
Reduction of polyatomic interferences in ICP-MS by collision/reaction cell (CRC-ICP-MS) techniques

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

Eiden, Greg C; Barinaga, Charles J; Koppenaal, David W

2012-05-01

Polyatomic and other spectral interferences in plasma source mass spectrometry (PSMS) can be dramatically reduced using collision and reaction cells (CRC). These devices have been used for decades in fundamental studies of ion-molecule chemistry, but have only recently been applied to PSMS. Benefits of this approach as applied in inductively coupled plasma MS (ICP-MS) include interference reduction, isobar separation, and thermalization/focusing of ions. Novel ion-molecule chemistry schemes are now routinely designed and empirically evaluated with relative ease. These “chemical resolution” techniques can avert interferences requiring mass spectral resolutions of >600,000 (m/m). Purely physical ion beam processes, including collisional dampening andmore » collisional dissociation, are also employed to provide improved sensitivity, resolution, and spectral simplicity. CRC techniques are now firmly entrenched in current-day ICP-MS technology, enabling unprecedented flexibility and freedom from many spectral interferences. A significant body of applications has now been reported in the literature. CRC techniques are found to be most useful for specialized or difficult analytical needs and situations, and are employed in both single- and multi-element determination modes.« less
An Update on the Non-Mass-Dependent Isotope Fractionation under Thermal Gradient

NASA Technical Reports Server (NTRS)

Sun, Tao; Niles, Paul; Bao, Huiming; Socki, Richard; Liu, Yun

2013-01-01

Mass flow and compositional gradient (elemental and isotope separation) occurs when flu-id(s) or gas(es) in an enclosure is subjected to a thermal gradient, and the phenomenon is named thermal diffusion. Gas phase thermal diffusion has been theoretically and experimentally studied for more than a century, although there has not been a satisfactory theory to date. Nevertheless, for isotopic system, the Chapman-Enskog theory predicts that the mass difference is the only term in the thermal diffusion separation factors that differs one isotope pair to another,with the assumptions that the molecules are spherical and systematic (monoatomic-like structure) and the particle collision is elastic. Our previous report indicates factors may be playing a role because the Non-Mass Dependent (NMD) effect is found for both symmetric and asymmetric, linear and spherical polyatomic molecules over a wide range of temperature (-196C to +237C). The observed NMD phenomenon in the simple thermal-diffusion experiments demands quantitative validation and theoretical explanation. Besides the pressure and temperature dependency illustrated in our previous reports, efforts are made in this study to address issues such as the role of convection or molecular structure and whether it is a transient, non-equilibrium effect only.

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

PubMed

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.
Coherent electron emission beyond Young-type interference from diatomic molecules

NASA Astrophysics Data System (ADS)

Agueny, H.; Makhoute, A.; Dubois, A.; Hansen, J. P.

2016-01-01

It has been known for more than 15 years that the differential cross section of electrons emitted from diatomic molecules during interaction with energetic charged particles oscillates as a function of electron momentum. The origin of the phenomenon is two-center interference, which naturally relates it back to the Young double-slit experiment. In addition to a characteristic frequency which can be described by lowest-order perturbation theories, the observation and origin of higher-order harmonics of the basic oscillation frequency has been much discussed. Here, we show that high harmonics of the fundamental Young-type oscillation frequency observed in electron spectra in fast ion-molecule collisions can be clearly exposed in numerical solutions of the time-dependent Schrödinger equation within a one-dimensional model. Momentum distribution of the ejected electron is analyzed and shows that the phenomenon emerges when the charged particle beam collides with diatomic molecules with substantial large internuclear distance. Frequency spectra from nonperturbative calculations for electron emission from Rb2+ and Cs2+ exhibit a pronounced high-order oscillation in contrast to similar close-coupling calculations performed on H2 targets. The electron emission from these heavy molecules contains second- and third-order harmonics which are fully reproduced in an analytic model based on the Born series. Extending to triatomic molecular targets displays an increased range of harmonics. This suggests that electron emission spectra from new experiments on heavy diatomic and linear polyatomic molecular targets may provide a unique insight into competing coherent emission mechanisms and their relative strength.
Metal atom oxidation laser

DOEpatents

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

1975-10-28

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. (auth)
HO2 rovibrational eigenvalue studies for nonzero angular momentum

NASA Astrophysics Data System (ADS)

Wu, Xudong T.; Hayes, Edward F.

1997-08-01

An efficient parallel algorithm is reported for determining all bound rovibrational energy levels for the HO2 molecule for nonzero angular momentum values, J=1, 2, and 3. Performance tests on the CRAY T3D indicate that the algorithm scales almost linearly when up to 128 processors are used. Sustained performance levels of up to 3.8 Gflops have been achieved using 128 processors for J=3. The algorithm uses a direct product discrete variable representation (DVR) basis and the implicitly restarted Lanczos method (IRLM) of Sorensen to compute the eigenvalues of the polyatomic Hamiltonian. Since the IRLM is an iterative method, it does not require storage of the full Hamiltonian matrix—it only requires the multiplication of the Hamiltonian matrix by a vector. When the IRLM is combined with a formulation such as DVR, which produces a very sparse matrix, both memory and computation times can be reduced dramatically. This algorithm has the potential to achieve even higher performance levels for larger values of the total angular momentum.
Astronomical chemistry.

PubMed

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.
Physics with Cold Molecules Using Buffer Gas Cooling: Precision Measurement, Collisions, and Laser Cooling

NASA Astrophysics Data System (ADS)

Hutzler, Nicholas R.; Doyle, John M.

2014-06-01

Cryogenic buffer gas cooled beams and cells can be used to study many species, from atoms and polar molecules to biomolecules. We report on recent applications of this technique to improve the limit on the electron electric dipole moment [1], load polar molecules into a magnetic trap through optical pumping [2], perform chirally sensitive microwave spectroscopy on polyatomic molecules [3], progress towards magneto-optical trapping of polar molecules [4], and studies of atom-molecule sticking [5]. [1] The ACME Collaboration: J. Baron et al., Science 343, p. 269 (2014) [2] B. Hemmerling et al., arXiv:1310.2669, to appear in Phys. Rev. Lett. [3] D. Patterson, M. Schnell, & J. M. Doyle, Nature 497, p. 475 (2013) [4] H. Lu et al., arXiv:1310.3239, to appear in New. J. Phys. [5] J. Piskorski et al., under preparation
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

DOE R&D Accomplishments Database

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.

PubMed

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).
Coherent Bichromatic Force Deflection of Molecules

NASA Astrophysics Data System (ADS)

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.
Dynamics of pulsed expansion of polyatomic gas cloud: Internal-translational energy transfer contribution

NASA Astrophysics Data System (ADS)

Morozov, A. A.

2007-08-01

Polyatomic gas cloud expansion under pulsed laser evaporation is studied on the basis of one-dimensional direct Monte Carlo simulation. The effect of rotational-translational (RT) and vibrational-translational (VT) energy transfer on dynamics of the cloud expansion is considered. Efficiency of VT energy transfer dependence on the amount of evaporated matter is discussed. To analyze VT energy transfer impact, the number of collisions per molecule during the expansion is calculated. The data are generally in good agreement with available analytical and numerical predictions. Dependencies of the effective number of vibrational degrees of freedom on the number of vibrationally inelastic collisions are obtained and generalized. The importance of the consideration of energy transfer from the internal degrees of freedom to the translational ones is illustrated by an example of pulsed laser evaporation of polytetrafluoroethylene (PTFE). Based on the obtained regularities, analysis of experimental data on pulsed laser evaporation of aniline is performed. The calculated aniline vibrational temperature correlates well with the experimentally measured one.
Benchmark quality total atomization energies of small polyatomic molecules

NASA Astrophysics Data System (ADS)

Martin, Jan M. L.; Taylor, Peter R.

1997-05-01

Successive coupled-cluster [CCSD(T)] calculations in basis sets of spdf, spdfg, and spdfgh quality, combined with separate Schwartz-type extrapolations A+B/(l+1/2)α of the self-consistent field (SCF) and correlation energies, permit the calculations of molecular total atomization energies (TAEs) with a mean absolute error of as low as 0.12 kcal/mol. For the largest molecule treated, C2H4, we find ∑D0=532.0 kcal/mol, in perfect agreement with experiment. The aug-cc-pV5Z basis set recovers on average about 99% of the valence correlation contribution to the TAE, and essentially the entire SCF contribution.
Construction of Ligand Group Orbitals for Polyatomics and Transition-Metal Complexes Using an Intuitive Symmetry-Based Approach

ERIC Educational Resources Information Center

Johnson, Adam R.

2013-01-01

A molecular orbital (MO) diagram, especially its frontier orbitals, explains the bonding and reactivity for a chemical compound. It is therefore important for students to learn how to construct one. The traditional methods used to derive these diagrams rely on linear algebra techniques to combine ligand orbitals into symmetry-adapted linear…
Rotational dynamics of polyatomic ions in aqueous solutions: From continuum model to mode-coupling theory, aided by computer simulations.

PubMed

Banerjee, Puja; Bagchi, Biman

2018-06-14

Due to the presence of the rotational mode and the distributed surface charges, the dynamical behavior of polyatomic ions in water differs considerably from those of the monatomic ions. However, their fascinating dynamical properties have drawn scant attention. We carry out theoretical and computational studies of a series of well-known polyatomic ions, namely, sulfate, nitrate, and acetate ions. All three ions exhibit different rotational diffusivity, with that of the nitrate ion being considerably larger than the other two. They all defy the hydrodynamic laws of size dependence. Study of the local structure around the ions provides valuable insight into the origin of these differences. We carry out a detailed study of the rotational diffusion of these ions by extensive computer simulation and by using the theoretical approaches of the dielectric friction developed by Fatuzzo-Mason (FM) and Nee-Zwanzig (NZ), and subsequently generalized by Alavi and Waldeck. A critical element of the FM-NZ theory is the decomposition of the total rotational friction, ζ Rot , into Stokes and dielectric parts. The study shows a dominant role of dielectric friction in the sense that if the ions are made neutral, the nature of diffusion changes and the values become much larger. Our analyses further reveal that the decomposition of total friction into the Stokes and dielectric friction breaks down for sulfate ions but remains semi-quantitatively valid for nitrate and acetate ions. We discuss the relationship between translational and rotational dielectric friction on rigid spherical ions. We develop a self-consistent mode-coupling theory (SC-MCT) formalism that could provide a unified view of rotational friction of polyatomic ions in polar medium. Our SC-MCT shows that the breakdown can be attributed to the change in the microscopic structural features. The mode-coupling theory helps in elucidating the role of coupling between translational and rotational motion of these ions. In fact, these two motions self-consistently determine the value of each other. The reference interaction site model-based MCT suggests an interesting relation between the torque-torque and the force-force time correlation function with the proportionality constant being determined by the geometry and the charge distribution of the polyatomic molecule. We point out several parallelisms between the theories of translational and rotation friction calculations of ions in polar liquids.
THE DYNAMICS OF HYDROGEN ATOM ABSTRACTION FROM POLYATOMIC MOLECULES.

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

LIU,X.; SUITS,A.G.

2002-11-21

The hydrogen atom abstraction reaction is an important fundamental process that is extensively involved in atmospheric and combustion chemistry. The practical significance of this type of reaction with polyatomic hydrocarbons is manifest, which has led to many kinetics studies. The detailed understanding of these reactions requires corresponding dynamics studies. However, in comparison to the A + HX {radical} AH + X reactions, the study of the dynamics of A + HR {yields} AH + R reactions is much more difficult, both experimentally and theoretically (here and in the following, A stands for an atom, X stands for a halogen atom,more » and R stands for a polyatomic hydrocarbon radical). The complication stems from the structured R, in contrast to the structureless X. First of all, there are many internal degrees of freedom in R that can participate in the reaction. In addition, there are different carbon sites from which an H atom can be abstracted, and the dynamics are correspondingly different; there are also multiple identical carbon sites in HR and in the picture of a local reaction, there exist competitions between neighboring H atoms, and so on. Despite this complexity, there have been continuing efforts to obtain insight into the dynamics of these reactions. In this chapter, some examples are presented, including the reactions of ground state H, Cl, and O atoms, with particular focus on our recent work using imaging to obtain the differential cross sections for these reactions.« less
Using quantum dynamics simulations to follow the competition between charge migration and charge transfer in polyatomic molecules

NASA Astrophysics Data System (ADS)

Spinlove, K. E.; Vacher, M.; Bearpark, M.; Robb, M. A.; Worth, G. A.

2017-01-01

Recent work, particularly by Cederbaum and co-workers, has identified the phenomenon of charge migration, whereby charge flow occurs over a static molecular framework after the creation of an electronic wavepacket. In a real molecule, this charge migration competes with charge transfer, whereby the nuclear motion also results in the re-distribution of charge. To study this competition, quantum dynamics simulations need to be performed. To break the exponential scaling of standard grid-based algorithms, approximate methods need to be developed that are efficient yet able to follow the coupled electronic-nuclear motion of these systems. Using a simple model Hamiltonian based on the ionisation of the allene molecule, the performance of different methods based on Gaussian Wavepackets is demonstrated.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Cui, Jie; Krems, Roman V.; Li, Zhiying

We use classical trajectory calculations to study the effects of the interaction strength and the geometry of rigid polyatomic molecules on the formation of long-lived collision complexes at low collision energies. We first compare the results of the calculations for collisions of benzene molecules with rare gas atoms He, Ne, Ar, Kr, and Xe. The comparison illustrates that the mean lifetimes of the collision complexes increase monotonically with the strength of the atom–molecule interaction. We then compare the results of the atom–benzene calculations with those for benzene–benzene collisions. The comparison illustrates that the mean lifetimes of the benzene–benzene collision complexesmore » are significantly reduced due to non-ergodic effects prohibiting the molecules from sampling the entire configuration space. We find that the thermally averaged lifetimes of the benzene–benzene collisions are much shorter than those for Xe with benzene and similar to those for Ne with benzene.« less
Interstellar molecules - Origin by catalytic reactions on grain surfaces. [compound distribution analysis

NASA Technical Reports Server (NTRS)

Anders, E.; Hayatsu, R.; Studier, M. H.

1974-01-01

To determine the compound distribution formed by surface catalysis, mixtures of CO, D2, and ND2 were heated with nickel-iron or montmorillonite clay catalysts for 49-214 hours at 250 to 300 C. Compounds identified include most of the known polyatomic interstellar molecules, as well as homologous series of acetylenes, dienes, alcohols, aldehydes, ketones, ethers, esters, nitriles, amines, etc., and cyclic compounds such as furans and pyrroles. These homologous series are uniquely characteristic of surface catalysis. A search for the heavier members of these series, predicted to occur at 1/10th to 1/1,000th the abundance of the lightest members, thus comprises a crucial test of this mechanism.
A spherical electron cloud hopping model for studying product branching ratios of dissociative recombination.

PubMed

Yu, Hua-Gen

2008-05-21

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

NASA Technical Reports Server (NTRS)

Mohan, H.

1979-01-01

This monograph is basically devoted to spectroscopic information of the molecules of planetary interest. Only those molecules have been dealt with which have been confirmed spectroscopically to be present in the atmosphere of major planets of our solar system and play an important role in the aeronomy of the respective planets. An introduction giving the general conditions of planets and their atmospheres including the gaseous molecules is given. Some typical planetary spectra is presented and supported with a discussion on some basic concepts of optical absorption and molecular parameters that are important to the study of planetary atmospheres. Quantities like dipole moments, transition probabilities, Einstein coefficients and line strengths, radiative life times, absorption cross sections, oscillator strengths, line widths and profiles, equivalent widths, growth curves, bond strengths, electronic transition moments, Franck-Condon factors and r-centroids, etc., are discussed. Spectroscopic information and relevant data of 6 diatomic (HF, HCL, CO, H2, O2, N2) and 6 polyatomic (CO2, N2), O3, HeO, NH3, CH4) molecules are presented.
Communication: XFAIMS—eXternal Field Ab Initio Multiple Spawning for electron-nuclear dynamics triggered by short laser pulses

DOE PAGES

Mignolet, Benoit; Curchod, Basile F. E.; Martinez, Todd J.

2016-11-17

Attoscience is an emerging field where attosecond pulses or few cycle IR pulses are used to pump and probe the correlated electron-nuclear motion of molecules. We present the trajectory-guided eXternal Field Ab Initio Multiple Spawning (XFAIMS) method that models such experiments “on-the-fly,” from laser pulse excitation to fragmentation or nonadiabatic relaxation to the ground electronic state. For the photoexcitation of the LiH molecule, we show that XFAIMS gives results in close agreement with numerically exact quantum dynamics simulations, both for atto- and femtosecond laser pulses. As a result, we then show the ability of XFAIMS to model the dynamics inmore » polyatomic molecules by studying the effect of nuclear motion on the photoexcitation of a sulfine (H 2CSO).« less

Direct simulation Monte Carlo modeling of relaxation processes in polyatomic gases

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

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

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 methodsmore » 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.« less
Direct simulation Monte Carlo modeling of relaxation processes in polyatomic gases

NASA Astrophysics Data System (ADS)

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

PubMed

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

NASA Astrophysics Data System (ADS)

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.
Ion-momentum imaging of dissociative attachment of electrons to molecules

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

Slaughter, D. S.; Belkacem, A.; McCurdy, C. W.

Here, we present an overview of experiments and theory relevant to dissociative electron attachment studied by momentum imaging. We describe several key examples of characteristic transient anion dynamics in the form of small polyatomic electron-molecule systems. In each of these examples the so-called axial recoil approximation is found to break down due to correlation of the electronic and nuclear degrees of freedom of the transient anion. Guided by anion fragment momentum measurements and predictions of the electron scattering attachment probability in the molecular frame, we demonstrate that accurate predictions of the dissociation dynamics can be achieved without a detailed investigationmore » of the surface topology of the relevant electronic states or the fragment trajectories on those surfaces.« less
Ion-momentum imaging of dissociative attachment of electrons to molecules

DOE PAGES

Slaughter, D. S.; Belkacem, A.; McCurdy, C. W.; ...

2016-10-24

Here, we present an overview of experiments and theory relevant to dissociative electron attachment studied by momentum imaging. We describe several key examples of characteristic transient anion dynamics in the form of small polyatomic electron-molecule systems. In each of these examples the so-called axial recoil approximation is found to break down due to correlation of the electronic and nuclear degrees of freedom of the transient anion. Guided by anion fragment momentum measurements and predictions of the electron scattering attachment probability in the molecular frame, we demonstrate that accurate predictions of the dissociation dynamics can be achieved without a detailed investigationmore » of the surface topology of the relevant electronic states or the fragment trajectories on those surfaces.« less
Anharmonic Potential Constants and Their Dependence Upon Bond Length

DOE R&D Accomplishments Database

Herschbach, D. R.; Laurie, V. W.

1961-01-01

Empirical study of cubic and quartic vibrational force constants for diatomic molecules shows them to be approximately exponential functions of internuclear distance. A family of curves is obtained, determined by the location of the bonded atoms in rows of the periodic table. Displacements between successive curves correspond closely to those in Badger's rule for quadratic force constants (for which the parameters are redetermined to accord with all data now available). Constants for excited electronic and ionic states appear on practically the same curves as those for the ground states. Predictions based on the diatomic correlations agree with the available cubic constants for bond stretching in polyatomic molecules, regardless of the type of bonding involved. Implications of these regularities are discussed. (auth)
Direct Visualization of Valence Electron Motion Using Strong-Field Photoelectron Holography

NASA Astrophysics Data System (ADS)

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

PubMed

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

2018-03-30

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 H_{2}^{+}, 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.
Core-mass nonadiabatic corrections to molecules: H2, H2+, and isotopologues.

PubMed

Diniz, Leonardo G; Alijah, Alexander; Mohallem, José Rachid

2012-10-28

For high-precision calculations of rovibrational states of light molecules, it is essential to include non-adiabatic corrections. In the absence of crossings of potential energy surfaces, they can be incorporated in a single surface picture through coordinate-dependent vibrational and rotational reduced masses. We present a compact method for their evaluation and relate in particular the vibrational mass to a well defined nuclear core mass derived from a Mulliken analysis of the electronic density. For the rotational mass we propose a simple, but very effective parametrization. The use of these masses in the nuclear Schrödinger equation yields numerical data for the corrections of a much higher quality than can be obtained with optimized constant masses, typically better than 0.1 cm(-1). We demonstrate the method for H(2), H(2)(+), and singly deuterated isotopologues. Isotopic asymmetry does not present any particular difficulty. Generalization to polyatomic molecules is straightforward.
Simulated infrared emission spectra of highly excited polyatomic molecules: a detailed model of the PAH-UIR hypothesis

NASA Technical Reports Server (NTRS)

Cook, D. J.; Saykally, R. J.

1998-01-01

A detailed description of the polycyclic aromatic hydrocarbon (PAH)/unidentified infrared band (UIR) mechanism is presented in which experimental spectral bandshape functions are used to simulate IR emission spectra for individual molecules. These spectra are additively superimposed to produce a conglomerate spectrum representative of a family of PAH molecules. Ab initio vibrational frequencies and intensities for nine PAHs (neutral and cationic) as large as ovalene are used in conjunction with measured bandshape and temperature-dependent redshift data to simulate the UIR bands. The calculated spectra of cations provide a closer match to the UIRs than do those of the neutrals. However, the PAH cations used in the simulations fail to reproduce the details of the UIR emission spectra. The discrepancies are potentially alleviated if both larger PAHs and a greater number of PAHs were included in the simulation.
Theoretical investigation of gas-surface interactions

NASA Technical Reports Server (NTRS)

Dyall, Kenneth G.

1990-01-01

A Dirac-Hartree-Fock code was developed for polyatomic molecules. The program uses integrals over symmetry-adapted real spherical harmonic Gaussian basis functions generated by a modification of the MOLECULE integrals program. A single Gaussian function is used for the nuclear charge distribution, to ensure proper boundary conditions at the nuclei. The Gaussian primitive functions are chosen to satisfy the kinetic balance condition. However, contracted functions which do not necessarily satisfy this condition may be used. The Fock matrix is constructed in the scalar basis and transformed to a jj-coupled 2-spinor basis before diagonalization. The program was tested against numerical results for atoms with a Gaussian nucleus and diatomic molecules with point nuclei. The energies converge on the numerical values as the basis set size is increased. Full use of molecular symmetry (restricted to D sub 2h and subgroups) is yet to be implemented.
Stereocontrol of attosecond time-scale electron dynamics in ABCU using ultrafast laser pulses: a computational study.

PubMed

Mignolet, B; Gijsbertsen, A; Vrakking, M J J; Levine, R D; Remacle, F

2011-05-14

The attosecond time-scale electronic dynamics induced by an ultrashort laser pulse is computed using a multi configuration time dependent approach in ABCU (C(10)H(19)N), a medium size polyatomic molecule with a rigid cage geometry. The coupling between the electronic states induced by the strong pulse is included in the many electron Hamiltonian used to compute the electron dynamics. We show that it is possible to implement control of the electron density stereodynamics in this medium size molecule by varying the characteristics of the laser pulse, for example by polarizing the electric field either along the N-C axis of the cage, or in the plane perpendicular to it. The excitation produces an oscillatory, non-stationary, electronic state that exhibits localization of the electron density in different parts of the molecule both during and after the pulse. The coherent oscillations of the non-stationary electronic state are also demonstrated through the alternation of the dipole moment of the molecule.
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

NASA Astrophysics Data System (ADS)

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

NASA Astrophysics Data System (ADS)

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

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

Hu, Qichi; Johnson, Christopher J.; Continetti, Robert E., E-mail: hguo@umn.edu, E-mail: rcontinetti@ucsd.edu

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 energiesmore » 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.« less
Data Needs for Stellar Atmosphere and Spectrum Modeling

NASA Technical Reports Server (NTRS)

Short, C. I.

2006-01-01

The main data need for stellar atmosphere and spectrum modeling remains atomic and molecular transition data, particularly energy levels and transition cross-sections. We emphasize that data is needed for bound-free (b - f) as well as bound-bound (b - b), and collisional as well as radiative transitions. Data is now needed for polyatomic molecules as well as atoms, ions, and diatomic molecules. In addition, data for the formation of, and extinction due to, liquid and solid phase dust grains is needed. A prioritization of species and data types is presented, and gives emphasis to Fe group elements, and elements important for the investigation of nucleosynthesis and Galactic chemical evolution, such as the -elements and n-capture elements. Special data needs for topical problems in the modeling of cool stars and brown dwarfs are described.
An advanced kinetic theory for morphing continuum with inner structures

NASA Astrophysics Data System (ADS)

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.
Chirp effects on impulsive vibrational spectroscopy: a multimode perspective.

PubMed

Wand, Amir; Kallush, Shimshon; Shoshanim, Ofir; Bismuth, Oshrat; Kosloff, Ronnie; Ruhman, Sanford

2010-03-07

The well-documented propensity of negatively-chirped pulses to enhance resonant impulsive Raman scattering has been rationalized in terms of a one pulse pump-dump sequence which "follows" the evolution of the excited molecules and dumps them back at highly displaced configurations. The aim of this study was to extend the understanding of this effect to molecules with many displaced vibrational modes in the presence of condensed surroundings. In particular, to define an optimally chirped pulse, to investigate what exactly it "follows" and to discover how this depends on the molecule under study. To this end, linear chirp effects on vibrational coherences in poly-atomics are investigated experimentally and theoretically. Chirped pump-impulsive probe experiments are reported for Sulforhodamine-B ("Kiton Red"), Betaine-30 and Oxazine-1 in ethanol solutions with <10 fs resolution. Numerical simulations, including numerous displaced modes and electronic dephasing, are conducted to reproduce experimental results. Through semi-quantitative reproduction of experimental results in all three systems we show that the effect of group velocity dispersion (GVD) on the buildup of ground state wave-packets depends on the pulse spectrum, on the displacements of vibrational modes upon excitation, on the detuning of the excitation pulses from resonance, and on electronic dephasing rates. Akin to scenarios described for frequency-domain resonance Raman, within the small-displacement regime each mode responds to excitation chirp independently and the optimal GVD is mode-specific. Highly-displaced modes entangle the dynamics of excitation in different modes, requiring a multi-dimensional description of the response. Rapid photochemistry and ultrafast electronic dephasing narrow the window of opportunity for coherent manipulations, leading to a reduced and similar optimal chirp for different modes. Finally, non-intuitive coherent aspects of chirp "following" are predicted in the small-displacement and slow-dephasing regime, which remain to be observed in experiment.
Mixed Quantum/Classical Theory for Molecule-Molecule Inelastic Scattering: Derivations of Equations and Application to N2 + H2 System.

PubMed

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.

Constrained-pairing mean-field theory. IV. Inclusion of corresponding pair constraints and connection to unrestricted Hartree-Fock theory.

PubMed

Tsuchimochi, Takashi; Henderson, Thomas M; Scuseria, Gustavo E; Savin, Andreas

2010-10-07

Our previously developed constrained-pairing mean-field theory (CPMFT) is shown to map onto an unrestricted Hartree-Fock (UHF) type method if one imposes a corresponding pair constraint to the correlation problem that forces occupation numbers to occur in pairs adding to one. In this new version, CPMFT has all the advantages of standard independent particle models (orbitals and orbital energies, to mention a few), yet unlike UHF, it can dissociate polyatomic molecules to the correct ground-state restricted open-shell Hartree-Fock atoms or fragments.
Coupled-cluster treatment of molecular strong-field ionization

NASA Astrophysics Data System (ADS)

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.
A table of polyatomic interferences in ICP-MS

USGS Publications Warehouse

May, Thomas W.; Wiedmeyer, Ray H.

1998-01-01

Spectroscopic interferences are probably the largest class of interferences in ICP-MS and are caused by atomic or molecular ions that have the same mass-to-charge as analytes of interest. Current ICP-MS instrumental software corrects for all known atomic “isobaric” interferences, or those caused by overlapping isotopes of different elements, but does not correct for most polyatomic interferences. Such interferences are caused by polyatomic ions that are formed from precursors having numerous sources, such as the sample matrix, reagents used for preparation, plasma gases, and entrained atmospheric gases.
Rotation driven translational diffusion of polyatomic ions in water: A novel mechanism for breakdown of Stokes-Einstein relation

NASA Astrophysics Data System (ADS)

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

PubMed

Banerjee, Puja; Yashonath, Subramanian; Bagchi, Biman

2017-04-28

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 (KNO 3 ) and aqueous potassium acetate (CH 3 COOK) solutions. The two ions, nitrate (NO3-) and acetate (CH 3 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.
Greenhouse effect in planetary atmospheres caused by molecular symmetry breaking in intermolecular interactions

NASA Astrophysics Data System (ADS)

Vigasin, A. A.; Mokhov, I. I.

2017-03-01

It is believed that the greenhouse effect is related to the parameters of absorption spectra of polyatomic molecules, usually trace gases, in planetary atmospheres. The main components of all known atmospheres of celestial bodies are symmetrical molecules that do not possess the dipole-allowed purely rotational (and in the case of diatomic molecules, vibrational-rotational) absorption spectrum. Upon increased pressure, a weak absorption appears, induced by intermolecular interaction, which can lead to a greenhouse effect. The contribution of the induced absorption in radiative forcing of a dense atmosphere may amount to a few or even tens of W/m2. In conditions typical for the atmospheres of terrestrial planets (including paleoatmospheres), the collision-induced absorption and associated greenhouse effect may lead to an increase in surface temperature above the freezing point of water. There is a correlation between the temperature of an atmosphere and the intermolecular bonding energy of gases that dominate in planetary atmospheres of the Solar System.
Quantum Theories of Self-Localization

NASA Astrophysics Data System (ADS)

Bernstein, Lisa Joan

In the classical dynamics of coupled oscillator systems, nonlinearity leads to the existence of stable solutions in which energy remains localized for all time. Here the quantum-mechanical counterpart of classical self-localization is investigated in the context of two model systems. For these quantum models, the terms corresponding to classical nonlinearities modify a subset of the stationary quantum states to be particularly suited to the creation of nonstationary wavepackets that localize energy for long times. The first model considered here is the Quantized Discrete Self-Trapping model (QDST), a system of anharmonic oscillators with linear dispersive coupling used to model local modes of vibration in polyatomic molecules. A simple formula is derived for a particular symmetry class of QDST systems which gives an analytic connection between quantum self-localization and classical local modes. This formula is also shown to be useful in the interpretation of the vibrational spectra of some molecules. The second model studied is the Frohlich/Einstein Dimer (FED), a two-site system of anharmonically coupled oscillators based on the Frohlich Hamiltonian and motivated by the theory of Davydov solitons in biological protein. The Born-Oppenheimer perturbation method is used to obtain approximate stationary state wavefunctions with error estimates for the FED at the first excited level. A second approach is used to reduce the first excited level FED eigenvalue problem to a system of ordinary differential equations. A simple theory of low-energy self-localization in the FED is discussed. The quantum theories of self-localization in the intrinsic QDST model and the extrinsic FED model are compared.
Deuterium enrichment in the primitive ices of the protosolar nebula

NASA Technical Reports Server (NTRS)

Lutz, Barry L.; Owen, Tobias; De Bergh, Catherine

1990-01-01

On the basis of CH3D/CH4-ratio observations in the outer planets, the present effort to estimate the D/H ratio of the protosolar nebula's primitive ices arrives at two simple, yet effectively limiting models which constrain the degree of dilution undergone by deuterated volatiles through mixing with the initial hydrogen envelopes. These volatiles would have been contributed to planetary atmospheres by evaporated primordial ices. Ice D/H ratio model results of 0.0001 to 0.001 are compared with values for other potentially primitive material-containing bodies in the solar system, as well as with D/H ratio values from interstellar polyatomic molecules.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Fujii, M.; Sato, K.; Kimura, K.

Photoelectron spectra due to autoionization for two series of high Rydberg states have been observed for diazabicyclooctane (DABCO) in a supersonic jet. The selection rule of the autoionization has been found to be ..delta..v = -1 for each vibrational mode involved in the Rydberg states, consistent with Berry's theory available for the vibrational autoionization of a polyatomic molecule. The relative autoionization efficiencies Phi/sub a/ for the high Rydberg series have also been determined from two-color MPI and fluorescence dip spectra. The irregular variation of Phi/sub a/ with the principal quantum number n has been found for the two Rydberg series,more » suggesting the irregular variation in their nonradiative rates« less
Nonunique and nonuniform mapping in few-body Coulomb-explosion imaging

NASA Astrophysics Data System (ADS)

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.
Imaging CF3I conical intersection and photodissociation dynamics by ultrafast electron diffraction

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

Yang, Jie

Conical intersections play a critical role in excited state dynamics of polyatomic molecules, as they govern the reaction pathways of many nonadiabatic processes. However, ultrafast probes have lacked sufficient spatial resolution to image wavepacket trajectories through these intersections directly. Here we present the simultaneous experimental characterization of one-photon and two-photon excitation channels in isolated CF3I molecules using ultrafast gas phase electron diffraction. In the two-photon channel, we have mapped out the real space trajectories of a coherent nuclear wavepacket, which bifurcates onto two potential energy surfaces when passing through a conical intersection. In the one-photon channel, we have resolved excitationmore » of both the umbrella and the breathing vibrational modes in the CF3 fragment in multiple nuclear dimensions. These findings benchmark and validate ab-initio nonadiabatic dynamics calculations.« less
Analysis of experimental heats of dilution of aqueous solutions of NaBPh 4 by use of the mean spherical approximation and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

M'halla, Jalel; M'halla, Sondes; Wipff, Georges

2003-03-01

Calorimetric measurements of heats of dilution: QDC→0 =- nsφL,sexp, of aqueous solutions of NaBPh 4 are determined at 25 °C in the concentration range: 0
Decelerating and Trapping Large Polar Molecules.

PubMed

Patterson, David

2016-11-18

Manipulating the motion of large polyatomic molecules, such as benzonitrile (C 6 H 5 CN), presents significant difficulties compared to the manipulation of diatomic molecules. Although recent impressive results have demonstrated manipulation, trapping, and cooling of molecules as large as CH 3 F, no general technique for trapping such molecules has been demonstrated, and cold neutral molecules larger than 5 atoms have not been trapped (M. Zeppenfeld, B. G. U. Englert, R. Glöckner, A. Prehn, M. Mielenz, C. Sommer, L. D. van Buuren, M. Motsch, G. Rempe, Nature 2012, 491, 570-573). In particular, extending Stark deceleration and electrostatic trapping to such species remains challenging. Here, we propose to combine a novel "asymmetric doublet state" Stark decelerator with recently demonstrated slow, cold, buffer-gas-cooled beams of closed-shell volatile molecules to realize a general system for decelerating and trapping samples of a broad range of volatile neutral polar prolate asymmetric top molecules. The technique is applicable to most stable volatile molecules in the 100-500 AMU range, and would be capable of producing trapped samples in a single rotational state and at a motional temperature of hundreds of mK. Such samples would immediately allow for spectroscopy of unprecedented resolution, and extensions would allow for further cooling and direct observation of slow intramolecular processes such as vibrational relaxation and Hertz-level tunneling dynamics. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Atomic Rearrangements in Electron Attachment to Laser-Excited Molecules^*

NASA Astrophysics Data System (ADS)

Pinnaduwage, Lal; McCorkle, Dennis

1996-10-01

We report the observation of extensive atomic rearrangements in dissociative electron attachment to triethylamine " (Pinnaduwage and McCorkle, Chem.Phys. Lett. (in press, 1996))" and benzene laser excited to energies above their ionization thresholds. Large signal of "rearranged" negative ions, such as C_3^- (which is observed in both cases), were observed. This is in contrast to negative-ion formation via electron attachment to molecules in their ground states, where "rearranged" negative ions are comparatively weak and have been observed only occasionally. However, formation of "rearranged" positive ions is of common occurrence in the ionization of polyatomic molecules; it is possible that the formation of "rearranged" positive ions in the ionization processes, and the formation of such negative ions via electron attachment to excited states located close to the ionization threshold, are related. * Work supported by the LDRD Program of the Oak Ridge National Laboratory, managed by Lockheed Martin Energy Research Corp. for the US Department of Energy under contract number DE-AC05-96OR22464, and by the National Science Foundation under contract CHE-93113949 with the Univ. of Tenn., Knoxville.
Ultrafast Dynamics of 1,3-Cyclohexadiene in Highly Excited States

DOE PAGES

Bühler, Christine C.; Minitti, Michael P.; Deb, Sanghamitra; ...

2011-01-01

The ultrafast dynamics of 1,3-cyclohexadiene has been investigated via structurally sensitive Rydberg electron binding energies and shown to differ upon excitation to the 1B state and the 3p Rydberg state. Excitation of the molecule with 4.63 eV photons into the ultrashort-lived 1B state yields the well-known ring opening to 1,3,5-hexatriene, while a 5.99 eV photon lifts the molecule directly into the 3p-Rydberg state. Excitation to 3p does not induce ring opening. In both experiments, time-dependent shifts of the Rydberg electron binding energy reflect the structural dynamics of the molecular core. Structural distortions associated with 3p-excitation cause a dynamical shift in the -more » and -binding energies by 10 and 26 meV/ps, respectively, whereas after excitation into 1B, more severe structural transformations along the ring-opening coordinate produce shifts at a rate of 40 to 60 meV/ps. The experiment validates photoionization-photoelectron spectroscopy via Rydberg states as a powerful technique to observe structural dynamics of polyatomic molecules.« less
Separated-pair independent particle model and the generalized Brillouin theorem: ab initio calculations on the dissociation of polyatomic molecules

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

Sundberg, Kenneth Randall

1976-01-01

A method is developed to optimize the separated-pair independent particle (SPIP) wave function; it is a special case of the separated-pair theory obtained by using two-term natural expansions of the geminals. The orbitals are optimized by a theory based on the generalized Brillouin theorem and iterative configuration interaction (CI) calculations in the space of the SPIP function and its single excitations. The geminal expansion coefficients are optimized by serial 2 x 2 CI calculations. Formulas are derived for the matrix elements. An algorithm to implement the method is presented, and the work needed to evaluate the molecular integrals is discussed.
Computer program for calculating and fitting thermodynamic functions

NASA Technical Reports Server (NTRS)

Mcbride, Bonnie J.; Gordon, Sanford

1992-01-01

A computer program is described which (1) calculates thermodynamic functions (heat capacity, enthalpy, entropy, and free energy) for several optional forms of the partition function, (2) fits these functions to empirical equations by means of a least-squares fit, and (3) calculates, as a function of temperture, heats of formation and equilibrium constants. The program provides several methods for calculating ideal gas properties. For monatomic gases, three methods are given which differ in the technique used for truncating the partition function. For diatomic and polyatomic molecules, five methods are given which differ in the corrections to the rigid-rotator harmonic-oscillator approximation. A method for estimating thermodynamic functions for some species is also given.
Comparison of different eigensolvers for calculating vibrational spectra using low-rank, sum-of-product basis functions

NASA Astrophysics Data System (ADS)

Leclerc, Arnaud; Thomas, Phillip S.; Carrington, Tucker

2017-08-01

Vibrational spectra and wavefunctions of polyatomic molecules can be calculated at low memory cost using low-rank sum-of-product (SOP) decompositions to represent basis functions generated using an iterative eigensolver. Using a SOP tensor format does not determine the iterative eigensolver. The choice of the interative eigensolver is limited by the need to restrict the rank of the SOP basis functions at every stage of the calculation. We have adapted, implemented and compared different reduced-rank algorithms based on standard iterative methods (block-Davidson algorithm, Chebyshev iteration) to calculate vibrational energy levels and wavefunctions of the 12-dimensional acetonitrile molecule. The effect of using low-rank SOP basis functions on the different methods is analysed and the numerical results are compared with those obtained with the reduced rank block power method. Relative merits of the different algorithms are presented, showing that the advantage of using a more sophisticated method, although mitigated by the use of reduced-rank SOP functions, is noticeable in terms of CPU time.
Role of electronic correlations in photoionization of NO2 in the vicinity of the 2A1/2B2 conical intersection.

PubMed

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.
Chemical Evolution of a Protoplanetary Disk

NASA Astrophysics Data System (ADS)

Semenov, Dmitry A.

2011-12-01

In this paper we review recent progress in our understanding of the chemical evolution of protoplanetary disks. Current observational constraints and theoretical modeling on the chemical composition of gas and dust in these systems are presented. Strong variations of temperature, density, high-energy radiation intensities in these disks, both radially and vertically, result in a peculiar disk chemical structure, where a variety of processes are active. In hot, dilute and heavily irradiated atmosphere only the most photostable simple radicals and atoms and atomic ions exist, formed by gas-phase processes. Beneath the atmosphere a partly UV-shielded, warm molecular layer is located, where high-energy radiation drives rich ion-molecule and radical-radical chemistry, both in the gas phase and on dust surfaces. In a cold, dense, dark disk midplane many molecules are frozen out, forming thick icy mantles where surface chemistry is active and where complex polyatomic (organic) species are synthesized. Dynamical processes affect disk chemical composition by enriching it in abundances of complex species produced via slow surface processes, which will become detectable with ALMA.

Nuclear relaxation and vibrational contributions to the static electrical properties of polyatomic molecules: beyond the Hartree-Fock approximation

NASA Astrophysics Data System (ADS)

Luis, Josep M.; Martí, Josep; Duran, Miquel; Andrés, JoséL.

1997-04-01

Electronic and nuclear contributions to the static molecular electrical properties, along with the Stark tuning rate ( δνE ) and the infrared cross section changes ( δSE) have been calculated at the SCF level and at different correlated levels of theory, using a TZ2P basis set and finite field techniques. Nuclear contributions to these molecular properties have also been calculated using a recent analytical approach that allow both to check the accuracy of the finite field values, and to evaluate the importance of higher-order derivatives. The HF, CO, H 2O, H 2CO, and CH 4 molecules have been studied and the results compared to experimental date when available. The paper shows that nuclear relaxation and vibrational contributions must be included in order to obtain accurate values of the static electrical properties. Two different, combined approaches are proposed to predict experimental values of the electrical properties to an error smaller than 5%.
Numerical-analytic implementation of the higher-order canonical Van Vleck perturbation theory for the interpretation of medium-sized molecule vibrational spectra.

PubMed

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.
Rigid rotators. [deriving the time-independent energy states associated with rotational motions of the molecule

NASA Technical Reports Server (NTRS)

1976-01-01

The two-particle, steady-state Schroedinger equation is transformed to center of mass and internuclear distance vector coordinates, leading to the free particle wave equation for the kinetic energy motion of the molecule and a decoupled wave equation for a single particle of reduced mass moving in a spherical potential field. The latter describes the vibrational and rotational energy modes of the diatomic molecule. For fixed internuclear distance, this becomes the equation of rigid rotator motion. The classical partition function for the rotator is derived and compared with the quantum expression. Molecular symmetry effects are developed from the generalized Pauli principle that the steady-state wave function of any system of fundamental particles must be antisymmetric. Nuclear spin and spin quantum functions are introduced and ortho- and para-states of rotators, along with their degeneracies, are defined. Effects of nuclear spin on entropy are deduced. Next, rigid polyatomic rotators are considered and the partition function for this case is derived. The patterns of rotational energy levels for nonlinear molecules are discussed for the spherical symmetric top, for the prolate symmetric top, for the oblate symmetric top, and for the asymmetric top. Finally, the equilibrium energy and specific heat of rigid rotators are derived.
Electron-molecule scattering in a strong laser field: Two-center interference effects

NASA Astrophysics Data System (ADS)

Dakić, J.; Habibović, D.; Čerkić, A.; Busuladžić, M.; Milošević, D. B.

2017-10-01

Laser-assisted scattering of electrons on diatomic molecules is considered using the S -matrix theory within the second Born approximation. The first term of the expansion in powers of the scattering potential corresponds to the direct or single laser-assisted scattering of electrons on molecular targets, while the second term of this expansion corresponds to the laser-assisted rescattering or double scattering. The rescattered electrons may have considerably higher energies in the final state than those that scattered only once. For multicenter polyatomic molecules scattering and rescattering may happen at any center and in any order. All these cases contribute to the scattering amplitude and the interference of different contributions leads to an increase or a decrease of the differential cross section in particular electron energy regions. For diatomic molecules there are two such contributions for single scattering and four contributions for double scattering. Analyzing the spectra of the scattered electrons, we find two interesting effects. For certain molecular orientations, the plateaus in the electron energy spectrum, characteristic of laser-assisted electron-atom scattering, are replaced by a sequence of gradually declining maxima, caused by the two-center interference effects. The second effect is the appearance of symmetric U -shaped structures in the angle-resolved energy spectra, which are described very well by the analytical formulas we provide.
Symbolic derivation of high-order Rayleigh-Schroedinger perturbation energies using computer algebra: Application to vibrational-rotational analysis of diatomic molecules

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

Herbert, John M.

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 formore » 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.« less
Non-adiabatic dynamics close to conical intersections and the surface hopping perspective

PubMed Central

Malhado, João Pedro; Bearpark, Michael J.; Hynes, James T.

2014-01-01

Conical intersections play a major role in the current understanding of electronic de-excitation in polyatomic molecules, and thus in the description of photochemistry and photophysics of molecular systems. This article reviews aspects of the basic theory underlying the description of non-adiabatic transitions at conical intersections, with particular emphasis on the important case when the dynamics of the nuclei are treated classically. Within this classical nuclear motion framework, the main aspects of the surface hopping methodology in the conical intersection context are presented. The emerging picture from this treatment is that of electronic transitions around conical intersections dominated by the interplay of the nuclear velocity and the derivative non-adiabatic coupling vector field. PMID:25485263
Determination of molecular spectroscopic parameters and energy-transfer rates by double-resonance spectroscopy

NASA Technical Reports Server (NTRS)

Steinfeld, J. I.; Foy, B.; Hetzler, J.; Flannery, C.; Klaassen, J.; Mizugai, Y.; Coy, S.

1990-01-01

The spectroscopy of small to medium-size polyatomic molecules can be extremely complex, especially in higher-lying overtone and combination vibrational levels. The high density of levels also complicates the understanding of inelastic collision processes, which is required to model energy transfer and collision broadening of spectral lines. Both of these problems can be addressed by double-resonance spectroscopy, i.e., time-resolved pump-probe measurements using microwave, infrared, near-infrared, and visible-wavelength sources. Information on excited-state spectroscopy, transition moments, inelastic energy transfer rates and propensity rules, and pressure-broadening parameters may be obtained from such experiments. Examples are given for several species of importance in planetary atmospheres, including ozone, silane, ethane, and ammonia.
Sensitivity of transitions in internal rotor molecules to a possible variation of the proton-to-electron mass ratio

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

Jansen, Paul; Ubachs, Wim; Bethlem, Hendrick L.

2011-12-15

Recently, methanol was identified as a sensitive target system to probe variations of the proton-to-electron mass ratio {mu}[Jansen et al., Phys. Rev. Lett. 106, 100801 (2011)]. The high sensitivity of methanol originates from the interplay between overall rotation and hindered internal rotation of the molecule; that is, transitions that convert internal rotation energy into overall rotation energy, or vice versa, have an enhanced sensitivity coefficient, K{sub {mu}}. As internal rotation is a common phenomenon in polyatomic molecules, it is likely that other molecules display similar or even larger effects. In this paper we generalize the concepts that form the foundationmore » of the high sensitivity in methanol and use this to construct an approximate model which makes it possible to estimate the sensitivities of transitions in internal rotor molecules with C{sub 3v} symmetry, without performing a full calculation of energy levels. We find that a reliable estimate of transition sensitivities can be obtained from the three rotational constants (A, B, and C) and three torsional constants (F, V{sub 3}, and {rho}). This model is verified by comparing obtained sensitivities for methanol, acetaldehyde, acetamide, methyl formate, and acetic acid with a full analysis of the molecular Hamiltonian. Of the molecules considered, methanol is by far the most suitable candidate for laboratory and cosmological tests searching for a possible variation of {mu}.« less
Shock-wave structure for a polyatomic gas with large bulk viscosity

NASA Astrophysics Data System (ADS)

Kosuge, Shingo; Aoki, Kazuo

2018-02-01

The structure of a standing plane shock wave in a polyatomic gas is investigated on the basis of kinetic theory, with special interest in gases with large bulk viscosities, such as CO2 gas. The ellipsoidal statistical model for a polyatomic gas is employed. First, the shock structure is computed numerically for various upstream Mach numbers and for various (large) values of the ratio of the bulk viscosity to the shear viscosity, and different types of profiles, such as the double-layer structure consisting of a thin upstream layer with a steep change and a much thicker downstream layer with a mild change, are obtained. Then, an asymptotic analysis for large values of the ratio is carried out, and an analytical solution that describes the different types of profiles obtained by the numerical analysis, such as the double-layer structure, correctly is obtained.
Use of a single trajectory to study product energy partitioning in unimolecular dissociation: mass effects for halogenated alkanes.

PubMed

Sun, Lipeng; Park, Kyoyeon; Song, Kihyung; Setser, Donald W; Hase, William L

2006-02-14

A single trajectory (ST) direct dynamics approach is compared with quasiclassical trajectory (QCT) direct dynamics calculations for determining product energy partitioning in unimolecular dissociation. Three comparisons are made by simulating C(2)H(5)F-->HF + C(2)H(4) product energy partitioning for the MP26-31G(*) and MP26-311 + + G(**) potential energy surfaces (PESs) and using the MP26-31G(*) PES for C(2)H(5)F dissociation as a model to simulate CHCl(2)CCl(3)-->HCl + C(2)Cl(4) dissociation and its product energy partitioning. The trajectories are initiated at the transition state with fixed energy in reaction-coordinate translation E(t) (double dagger). The QCT simulations have zero-point energy (ZPE) in the vibrational modes orthogonal to the reaction coordinate, while there is no ZPE for the STs. A semiquantitative agreement is obtained between the ST and QCT average percent product energy partitionings. The ST approach is used to study mass effects for product energy partitioning in HX(X = F or Cl) elimination from halogenated alkanes by using the MP26-31G(*) PES for C(2)H(5)F dissociation and varying the masses of the C, H, and F atoms. There is, at most, only a small mass effect for partitioning of energy to HX vibration and rotation. In contrast, there are substantial mass effects for partitioning to relative translation and the polyatomic product's vibration and rotation. If the center of mass of the polyatomic product is located away from the C atom from which HX recoils, the polyatomic has substantial rotation energy. Polyatomic products, with heavy atoms such as Cl atoms replacing the H atoms, receive substantial vibration energy that is primarily transferred to the wag-bend motions. For E(t) (double dagger) of 1.0 kcalmol, the ST calculations give average percent partitionings to relative translation, polyatomic vibration, polyatomic rotation, HX vibration, and HX rotation of 74.9%, 6.8%, 1.5%, 14.4%, and 2.4% for C(2)H(5)F dissociation and 39.7%, 38.1%, 0.2%, 16.1%, and 5.9% for a model of CHCl(2)CCl(3) dissociation.
Mass Spectrometry as a Preparative Tool for the Surface Science of Large Molecules

NASA Astrophysics Data System (ADS)

Rauschenbach, Stephan; Ternes, Markus; Harnau, Ludger; Kern, Klaus

2016-06-01

Measuring and understanding the complexity that arises when nanostructures interact with their environment are one of the major current challenges of nanoscale science and technology. High-resolution microscopy methods such as scanning probe microscopy have the capacity to investigate nanoscale systems with ultimate precision, for which, however, atomic scale precise preparation methods of surface science are a necessity. Preparative mass spectrometry (pMS), defined as the controlled deposition of m/z filtered ion beams, with soft ionization sources links the world of large, biological molecules and surface science, enabling atomic scale chemical control of molecular deposition in ultrahigh vacuum (UHV). Here we explore the application of high-resolution scanning probe microscopy and spectroscopy to the characterization of structure and properties of large molecules. We introduce the fundamental principles of the combined experiments electrospray ion beam deposition and scanning tunneling microscopy. Examples for the deposition and investigation of single particles, for layer and film growth, and for the investigation of electronic properties of individual nonvolatile molecules show that state-of-the-art pMS technology provides a platform analog to thermal evaporation in conventional molecular beam epitaxy. Additionally, it offers additional, unique features due to the use of charged polyatomic particles. This new field is an enormous sandbox for novel molecular materials research and demands the development of advanced molecular ion beam technology.
NASA Astrophysics Data System (ADS)

2017-11-01

To deal with these problems investigators usually rely on a calibration method that makes use of a substance with an accurately known set of interatomic distances. The procedure consists of carrying out a diffraction experiment on the chosen calibrating substance, determining the value of the distances with use of the nominal (meter) value of the voltage, and then correcting the nominal voltage by an amount that produces the distances in the calibration substance. Examples of gases that have been used for calibration are carbon dioxide, carbon tetrachloride, carbon disulfide, and benzene; solids such as zinc oxide smoke (powder) deposited on a screen or slit have also been used. The question implied by the use of any standard molecule is, how accurate are the interatomic distance values assigned to the standard? For example, a solid calibrant is subject to heating by the electron beam, possibly producing unknown changes in the lattice constants, and polyatomic gaseous molecules require corrections for vibrational averaging ("shrinkage") effects that are uncertain at best. It has lately been necessary for us to investigate this matter in connection with on-going studies of several molecules in which size is the most important issue. These studies indicated that our usual method for retrieval of data captured on film needed improvement. The following is an account of these two issues - the accuracy of the distances assigned to the chosen standard molecule, and the improvements in our methods of retrieving the scattered intensity data.
Chemiluminescence in cryogenic matrices

NASA Astrophysics Data System (ADS)

Lotnik, S. V.; Kazakov, Valeri P.

1989-04-01

The literature data on chemiluminescence (CL) in cryogenic matrices have been classified and correlated for the first time. The role of studies on phosphorescence and CL at low temperatures in the development of cryochemistry is shown. The features of low-temperature CL in matrices of nitrogen and inert gases (fine structure of spectra, matrix effects) and the data on the mobility and reactivity of atoms and radicals at very low temperatures are examined. The trends in the development of studies on CL in cryogenic matrices, such as the search for systems involving polyatomic molecules and extending the forms of CL reactions, are followed. The reactions of active nitrogen with hydrocarbons that are accompanied by light emission and CL in the oxidation of carbenes at T >= 77 K are examined. The bibliography includes 112 references.
Spectral difference Lanczos method for efficient time propagation in quantum control theory

NASA Astrophysics Data System (ADS)

Farnum, John D.; Mazziotti, David A.

2004-04-01

Spectral difference methods represent the real-space Hamiltonian of a quantum system as a banded matrix which possesses the accuracy of the discrete variable representation (DVR) and the efficiency of finite differences. When applied to time-dependent quantum mechanics, spectral differences enhance the efficiency of propagation methods for evolving the Schrödinger equation. We develop a spectral difference Lanczos method which is computationally more economical than the sinc-DVR Lanczos method, the split-operator technique, and even the fast-Fourier-Transform Lanczos method. Application of fast propagation is made to quantum control theory where chirped laser pulses are designed to dissociate both diatomic and polyatomic molecules. The specificity of the chirped laser fields is also tested as a possible method for molecular identification and discrimination.
Fragmentation of Small Molecules by Photo-Double Ionization

NASA Astrophysics Data System (ADS)

Osipov, Timur

2008-05-01

Molecular structure, formation, breakup pathways and recombination formed the subject of many theoretical and experimental studies. Among molecular species like H2, CO, N2, O2 recently great attention has been paid to the dynamics of the fragmentations and rearrangements of C2H2 molecule. Nature's smallest stable hydrocarbon, the symmetric linear acetylene molecule, C2H2, is an important polyatomic system for the study of photo initiated processes. Important features of the intramolecular dynamics in neutral acetylene have been revealed over many years through numerous spectroscopic studies. More recently, the availability of synchrotron radiation and intense laser sources has lead to intriguing studies of the ionization, isomerization and breakup dynamics of acetylene ions. Of particular interest are the yields into the symmetric (CH^+/CH^+), deprotonation (HCC^+/H^+) and quasi-symmetric (HHC^+/C^+) channels, the latter involving isomerization from the neutral acetylene structure into the vinylidene configuration prior to breakup. One expects that the products of dissociation, their kinetic energy releases (KER) and the isomerization times will depend on the particular initial electronic states of the dication involved, but such detailed information has heretofore not been available. We will present the results of the experiment where the dication of acetylene is prepared by Auger decay following core-level X-ray photoionization. Cold Target Recoil Ion Momentum Spectroscopy technique was used to measure the corresponding 3d momentum vectors of Auger electrons and recoil ions in coincidence. We will show that this experimental approach, in combination with ab initio quantum mechanical calculations, can yield a comprehensive map of the two-body dissociation pathways including transition through different electronic energy surfaces, barriers to direct dissociation and the associated rearrangement channels. Work done in collaboration with T. Rescigno, T. Weber, S. Miyabe, M. Hertlein, B. Feinberg, M. Prior, and A. Belkacem, Lawrence Berkeley National Laboratory; T. Jahnke, O. Jagutzki, L. Schmidt, M. Sch"offler, L. Foucar, S. Sch"ossler, T. Havermeier, S. Voss, and R. D"orner, Institut fur Kernphysik, J. W. Goethe-Universitat Frankfurt am Main; A. Landers, Auburn University, Alabama; A. Alnaser, Kansas State University; and L. Cocke, Kansas State University.
High Pressure Noble Gas Alkali Vapor Mixtures and Their Visible and Infrared Excimer Bands.

DTIC Science & Technology

1980-02-01

Curry, and W. Bapper, "Visible emission bands of KXen polyatomic exciplexes ," Phys. Rev. Letters 41, 543 (1978). A. C. Tam, T. Yabuzaki, S. M. Curry...I178 Visible Emission Bands of KXe. Polyatomic Exciplexes ’. Yauviki.’ ) A. C. Tam, 0’ S. M. Curry, ( ) and W. liapper COdumble Ru’Iiati.op labor,, ,wy...giound electronic states. These temperature. " exciplex " molectle, are often gool laser species (2) The polyxetide band broadens substantially since the
Channel-resolved photo- and Auger-electron spectroscopy of halogenated hydrocarbons

NASA Astrophysics Data System (ADS)

Ablikim, Utuq; Kaderiya, B.; Kumarapan, V.; Kushawaha, R.; Rudenko, A.; Rolles, D.; Xiong, H.; Berrah, N.; Bomme, C.; Savelyev, E.; Kilcoyne, D.

2016-05-01

Inner-shell photoelectron and Auger electron spectra of polyatomic molecules such as halogenated hydrocarbons are typically hard to interpret and assign due to many overlapping states that form broad bands even in high-resolution measurements. With the help of electron-ion-ion coincidence measurements performed using the velocity map imaging technique, we are able to detect high-energy (<= 150 eV) photo- and Auger electrons in coincidence with two- or many-body ionic fragmentation channels. Such channel-resolved measurements allow disentangling the overlapping electronic structures and help assigning individual components of the electron spectra to specific potential surfaces and final states. In this work, we present measurements on CH3 I, CH2 IBr, and CH2 ICl molecules in the gas-phase using soft x-ray light provided by the Advanced Light Source at LBNL. This project is supported by the DOE, Office of Science, BES, Division of Chemical, Geological and Biological Sciences under Award Number DE-FG02-86ER13491 (U.A., B.K., V.K., A.R., D.R.) and Award Number DE-SC0012376 (H.X., N.B.).
Millimeter-wave Absorption Studies of Molecules in Diffuse Clouds

NASA Astrophysics Data System (ADS)

Lucas, Robert; Liszt, Harvey S.

1999-10-01

With IRAM instruments in the last few years, we have been using compact extragalactic millimeter wave radio sources as background objects to study the absorption spectrum of diffuse interstellar gas at millimeter wavelengths. The molecular content of interstellar gas has turned out to be unexpectedly rich. Simple polyatomic molecules such as HCO+, C2H are quite ubiquitous near the Galactic plane (beta < 15o), and many species are detected in some directions (CO, HCO+, H2CO, HCN, HNC, CN, C2H, C3H2, H2S, CS, HCS+, SO, SiO). Remarkable proportionality relations are found between related species such as HCO+ and OH, or CN, HCN and HNC. The high abundance of some species is still a challenge for current models of diffuse cloud chemistry. A factor of 10 increase in the sensitivity will make such studies achievable in denser clouds, where the chemistry is still more active and where abundances are nowadays only available by emission measurements, and thus subject to uncertainties due to sometimes poorly understood line formation and excitation conditions.
Rovibrational spectroscopy using a kinetic energy operator in Eckart frame and the multi-configuration time-dependent Hartree (MCTDH) approach

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

Sadri, Keyvan, E-mail: keyvan.sadri@pci.uni-heidelberg.de; Meyer, Hans-Dieter, E-mail: hans-dieter.meyer@pci.uni-heidelberg.de; Lauvergnat, David, E-mail: david.lauvergnat@u-psud.fr

2014-09-21

For computational rovibrational spectroscopy the choice of the frame is critical for an approximate separation of overall rotation from internal motions. To minimize the coupling between internal coordinates and rotation, Eckart proposed a condition [“Some studies concerning rotating axes and polyatomic molecules,” Phys. Rev. 47, 552–558 (1935)] and a frame that fulfills this condition is hence called an Eckart frame. A method is developed to introduce in a systematic way the Eckart frame for the expression of the kinetic energy operator (KEO) in the polyspherical approach. The computed energy levels of a water molecule are compared with those obtained usingmore » a KEO in the standard definition of the Body-fixed frame of the polyspherical approach. The KEO in the Eckart frame leads to a faster convergence especially for large J states and vibrationally excited states. To provide an example with more degrees of freedom, rotational states of the vibrational ground state of the trans nitrous acid (HONO) are also investigated.« less
2012 Gordon Research Conference on Vibrational Spectroscopy - Formal Schedule and Speaker/Poster Program

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

Geiger, Franz

2012-08-10

The Vibrational Spectroscopy conference brings together experimentalists and theoreticians working at the frontiers of modern vibrational spectroscopy, with a special emphasis on spectroscopies that probe the structure and dynamics of molecules in gases, liquids, and at interfaces. The conference explores the wide range of state-of-the-art techniques based on vibrational motion. These techniques span the fields of time-domain, high-resolution frequency-domain, spatially-resolved, nonlinear, and multidimensional spectroscopies. The conference highlights both the application of these techniques in chemistry, materials, biology, the environment, and medicine as well as the development of theoretical models that enable one to connect spectroscopic signatures to underlying molecular motionsmore » including chemical reaction dynamics. The conference goal is to advance the field of vibrational spectroscopy by bringing together a collection of researchers who share common interests and who will gain from discussing work at the forefront of several connected areas. The intent is to emphasize the insights and understanding that studies of vibrations provide about a variety of molecular systems ranging from small polyatomic molecules to large biomolecules, nanomaterials, and environmental systems.« less

Final Report

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

McLuckey, Scott

2016-08-30

The overall objectives of this research effort were to expand the capabilities of spectroscopic and ion chemistry tools for the structural characterization of polyatomic ions of relevance to the broad mission of the Department of Energy. Mass spectrometry currently plays an important role in virtually all of the molecular sciences by virtue of the value of the accurate measurement of mass and the structural information that can be derived from various structural probes based on, for example, ion chemistry, ion mobility, and ion spectroscopy. Mass spectrometry has long played important roles in supporting the missions of the Department of Energymore » and its predecessor agencies, particularly in the area of isotopic analysis of nuclides. Molecular mass spectrometry has played increasingly important roles is many aspects of the production and use of energy as the nation has diversified its energy portfolio. There is an ongoing need for the expansion of the measurement capabilities associated with molecular mass spectrometry that involves both technological developments as well as improved understanding of the chemical and physical processes that take place upon ionization and ion analysis in a mass spectrometer. Advances in mass spectrometry have impacted science broadly and further advances will be required to meet the needs of current energy and environmental research. This program has historically focused on the structural characterization of polyatomic ions, usually within the context of a tandem mass spectrometry experiment. A wide variety of physical and chemical processes can take place within a mass spectrometer and advantage can be taken of such processes to enhance the quality and quantity of information that can be derived for a given chemical system of interest. For example, ions can undergo interactions with neutral molecules/atoms, light, surfaces, electrons, or oppositely charged ions. The outcomes of all such interactions can be sensitive to the structures of the ions and are therefore candidates for probes of ion structure. This program has historically focused on the chemistry and physics associated with ion/neutral interactions at both low and high translational energies, and ion/ion reactions. The former area has involved the study of ion/molecule reactions at thermal energies and the extensive study of collisional activation under a wide variety of conditions. A major area of emphasis has been collisional activation in electrodynamic ion traps. The study of gas-phase ion/ion reactions within the context of tandem mass spectrometry was initiated in this program and has grown to be a major research area in this group. Most of the focus in ion/ion chemistry has been on proton transfer and electron transfer reactions and some of the work in the previous budget period was directed, in particular, to fundamental aspects of electron transfer. Recently, the discovery of selective covalent ion/ion reactions has opened up new vistas for research that will expand significantly the capabilities of tandem mass spectrometry for the structural characterization of polyatomic ions.« less
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.

PubMed

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

2015-08-07

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 patterning of GaAs under irradiation with very heavy polyatomic Au ions

NASA Astrophysics Data System (ADS)

Bischoff, L.; Böttger, R.; Heinig, K.-H.; Facsko, S.; Pilz, W.

2014-08-01

Self-organization of surface patterns on GaAs under irradiation with heavy polyatomic Au ions has been observed. The patterns depend on the ion mass, and the substrate temperature as well as the incidence angle of the ions. At room temperature, under normal incidence the surface remains flat, whereas above 200 °C nanodroplets of Ga appear after irradiation with monatomic, biatomic as well as triatomic Au ions of kinetic energies in the range of 10-30 keV per atom. In the intermediate temperature range of 100-200 °C meander- and dot-like patterns form, which are not related to Ga excess. Under oblique ion incidence up to 45° from the surface normal, at room temperature the surface remains flat for mon- and polyatomic Au ions. For bi- and triatomic ions in the range of 60° ≤ α ≤ 70° ripple patterns have been found, which become shingle-like for α ≥ 80°, whereas the surface remains flat for monatomic ions.
Dynamics of photoionization from molecular electronic wavepacket states in intense pulse laser fields: A nonadiabatic electron wavepacket study.

PubMed

Matsuoka, Takahide; Takatsuka, Kazuo

2017-04-07

A theory for dynamics of molecular photoionization from nonadiabatic electron wavepackets driven by intense pulse lasers is proposed. Time evolution of photoelectron distribution is evaluated in terms of out-going electron flux (current of the probability density of electrons) that has kinetic energy high enough to recede from the molecular system. The relevant electron flux is in turn evaluated with the complex-valued electronic wavefunctions that are time evolved in nonadiabatic electron wavepacket dynamics in laser fields. To uniquely rebuild such wavefunctions with its electronic population being lost by ionization, we adopt the complex-valued natural orbitals emerging from the electron density as building blocks of the total wavefunction. The method has been implemented into a quantum chemistry code, which is based on configuration state mixing for polyatomic molecules. Some of the practical aspects needed for its application will be presented. As a first illustrative example, we show the results of hydrogen molecule and its isotope substitutes (HD and DD), which are photoionized by a two-cycle pulse laser. Photon emission spectrum associated with above threshold ionization is also shown. Another example is taken from photoionization dynamics from an excited state of a water molecule. Qualitatively significant effects of nonadiabatic interaction on the photoelectron spectrum are demonstrated.
Polyatomic ions from a high current ion implanter driven by a liquid metal ion source.

PubMed

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 Bi 2 + ions at room temperature from a GaBi capillary LMAIS will be presented and discussed.
Polyatomic ions from a high current ion implanter driven by a liquid metal ion source

NASA Astrophysics Data System (ADS)

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.
RichMol: A general variational approach for rovibrational molecular dynamics in external electric fields

NASA Astrophysics Data System (ADS)

Owens, Alec; Yachmenev, Andrey

2018-03-01

In this paper, a general variational approach for computing the rovibrational dynamics of polyatomic molecules in the presence of external electric fields is presented. Highly accurate, full-dimensional variational calculations provide a basis of field-free rovibrational states for evaluating the rovibrational matrix elements of high-rank Cartesian tensor operators and for solving the time-dependent Schrödinger equation. The effect of the external electric field is treated as a multipole moment expansion truncated at the second hyperpolarizability interaction term. Our fully numerical and computationally efficient method has been implemented in a new program, RichMol, which can simulate the effects of multiple external fields of arbitrary strength, polarization, pulse shape, and duration. Illustrative calculations of two-color orientation and rotational excitation with an optical centrifuge of NH3 are discussed.
The creation of hypersonic flows by a powerful impulse capillary discharge

NASA Astrophysics Data System (ADS)

Pashchina, A. S.; Karmatsky, R. E.; Klimov, A. I.

2017-11-01

The possibility of using a powerful pulsed capillary discharge to produce quasi-stationary highspeed plasma flows with characteristic Mach numbers M = 3-10 and temperatures T = 3000-6000 K has been experimentally substantiated. In a rarefied gas atmosphere ( p ∞ < 10 Torr), the transverse size of flow exceeds d < 3 cm and the duration of the working cycle can be brought to hundreds of milliseconds, which is of interest in problems of laboratory modeling of physical-chemical and gas-dynamic effects of interaction of bodies with hypersonic flows. Strong temperature nonequilibrium has been found (with the ratio between the vibrational and rotational temperatures reaching T v/ T r = 3 and more) and anomalously low values of the effective adiabatic index, which indicates an intensive formation of polyatomic molecules and condensed particles in a carbon-containing plasma.
Creation of Rydberg Polarons in a Bose Gas

NASA Astrophysics Data System (ADS)

Camargo, F.; Schmidt, R.; Whalen, J. D.; Ding, R.; Woehl, G.; Yoshida, S.; Burgdörfer, J.; Dunning, F. B.; Sadeghpour, H. R.; Demler, E.; Killian, T. C.

2018-02-01

We report spectroscopic observation of Rydberg polarons in an atomic Bose gas. Polarons are created by excitation of Rydberg atoms as impurities in a strontium Bose-Einstein condensate. They are distinguished from previously studied polarons by macroscopic occupation of bound molecular states that arise from scattering of the weakly bound Rydberg electron from ground-state atoms. The absence of a p -wave resonance in the low-energy electron-atom scattering in Sr introduces a universal behavior in the Rydberg spectral line shape and in scaling of the spectral width (narrowing) with the Rydberg principal quantum number, n . Spectral features are described with a functional determinant approach (FDA) that solves an extended Fröhlich Hamiltonian for a mobile impurity in a Bose gas. Excited states of polyatomic Rydberg molecules (trimers, tetrameters, and pentamers) are experimentally resolved and accurately reproduced with a FDA.
Entropy, energy, and entanglement of localized states in bent triatomic molecules

NASA Astrophysics Data System (ADS)

Yuan, Qiang; Hou, Xi-Wen

2017-05-01

The dynamics of quantum entropy, energy, and entanglement is studied for various initial states in an important spectroscopic Hamiltonian of bent triatomic molecules H2O, D2O, and H2S. The total quantum correlation is quantified in terms of the mutual information and the entanglement by the concurrence borrowed from the theory of quantum information. The Pauli entropy and the intramolecular energy usually used in the theory of molecules are calculated to establish a possible relationship between both theories. Sections of two quantities among these four quantities are introduced to visualize such relationship. Analytic and numerical simulations demonstrate that if an initial state is taken to be the stretch- or the bend-vibrationally localized state, the mutual information, the Pauli entropy, and the concurrence are dominant-positively correlated while they are dominantly anti-correlated with the interacting energy among three anharmonic vibrational modes. In particular, such correlation is more distinct for the localized state with high excitations in the bending mode. The nice quasi-periodicity of those quantities in D2O molecule reveals that this molecule prepared in the localized state in the stretching or the bending mode can be more appreciated for molecular quantum computation. However, the dynamical correlations of those quantities behave irregularly for the dislocalized states. Moreover, the hierarchy of the mutual information and the Pauli entropy is explicitly proved. Quantum entropy and energy in every vibrational mode are investigated. Thereby, the relation between bipartite and tripartite entanglements is discussed as well. Those are useful for the understanding of quantum correlations in high-dimensional states in polyatomic molecules from quantum information and intramolecular dynamics.
Can Internal Conversion BE Controlled by Mode-Specific Vibrational Excitation in Polyatomic Molecules

NASA Astrophysics Data System (ADS)

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.
POTENTIOLOGY (noun): study focusing on the development of new interatomic pair potential forms; sometimes pursued in an obsessive compulsive manner [The New Yorel Dictionary (2002, unpublished)].} IN SPECTROSCOPY: IT MATTERS

NASA Astrophysics Data System (ADS)

Le Roy, Robert J.

2009-06-01

Spectroscopists have long attempted to summarize what they know about small molecules in terms of a knowledge of potential energy curves or surfaces. For most of the past century, this involved deducing polynomial-expansion force-field coefficients from energy level expressions fitted to experimental data, or for diatomic molecules, by generating tables of many-digit RKR turning points from such expressions. In recent years, however, it has become increasingly common either to use high-level ab initio calculations to compute the desired potentials, or to determine parametrized global analytic potential functions from direct fits to spectroscopic data. In the former case, this invoked a need for robust, flexible, compact, and `portable' analytic potentials for summarizing the information contained in the (sometimes very large numbers of) ab initio points, and making them `user friendly'. In the latter case, the same properties are required for potentials used in the least-squares fitting procedure. In both cases, there is also a cardinal need for potential function forms that extrapolate sensibly, beyond the range of the experimental data or ab initio points. This talk will describe some recent developments in this area, and make a case for what is arguably the `best' general-purpose analytic potential function form now available. Applications to both diatomic molecules and simple polyatomic molecules will be discussed. footnote
Structure factors for tunneling ionization rates of molecules: General Hartree-Fock-based integral representation

NASA Astrophysics Data System (ADS)

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.
Preparation and coherent manipulation of pure quantum states of a single molecular ion

NASA Astrophysics Data System (ADS)

Chou, Chin-Wen; Kurz, Christoph; Hume, David B.; Plessow, Philipp N.; Leibrandt, David R.; Leibfried, Dietrich

2017-05-01

Laser cooling and trapping of atoms and atomic ions has led to advances including the observation of exotic phases of matter, the development of precision sensors and state-of-the-art atomic clocks. The same level of control in molecules could also lead to important developments such as controlled chemical reactions and sensitive probes of fundamental theories, but the vibrational and rotational degrees of freedom in molecules pose a challenge for controlling their quantum mechanical states. Here we use quantum-logic spectroscopy, which maps quantum information between two ion species, to prepare and non-destructively detect quantum mechanical states in molecular ions. We develop a general technique for optical pumping and preparation of the molecule into a pure initial state. This enables us to observe high-resolution spectra in a single ion (CaH+) and coherent phenomena such as Rabi flopping and Ramsey fringes. The protocol requires a single, far-off-resonant laser that is not specific to the molecule, so many other molecular ions, including polyatomic species, could be treated using the same methods in the same apparatus by changing the molecular source. Combined with the long interrogation times afforded by ion traps, a broad range of molecular ions could be studied with unprecedented control and precision. Our technique thus represents a critical step towards applications such as precision molecular spectroscopy, stringent tests of fundamental physics, quantum computing and precision control of molecular dynamics.
Preparation and coherent manipulation of pure quantum states of a single molecular ion.

PubMed

Chou, Chin-Wen; Kurz, Christoph; Hume, David B; Plessow, Philipp N; Leibrandt, David R; Leibfried, Dietrich

2017-05-10

Laser cooling and trapping of atoms and atomic ions has led to advances including the observation of exotic phases of matter, the development of precision sensors and state-of-the-art atomic clocks. The same level of control in molecules could also lead to important developments such as controlled chemical reactions and sensitive probes of fundamental theories, but the vibrational and rotational degrees of freedom in molecules pose a challenge for controlling their quantum mechanical states. Here we use quantum-logic spectroscopy, which maps quantum information between two ion species, to prepare and non-destructively detect quantum mechanical states in molecular ions. We develop a general technique for optical pumping and preparation of the molecule into a pure initial state. This enables us to observe high-resolution spectra in a single ion (CaH + ) and coherent phenomena such as Rabi flopping and Ramsey fringes. The protocol requires a single, far-off-resonant laser that is not specific to the molecule, so many other molecular ions, including polyatomic species, could be treated using the same methods in the same apparatus by changing the molecular source. Combined with the long interrogation times afforded by ion traps, a broad range of molecular ions could be studied with unprecedented control and precision. Our technique thus represents a critical step towards applications such as precision molecular spectroscopy, stringent tests of fundamental physics, quantum computing and precision control of molecular dynamics.
Gaussian process model for extrapolation of scattering observables for complex molecules: From benzene to benzonitrile

NASA Astrophysics Data System (ADS)

Cui, Jie; Li, Zhiying; Krems, Roman V.

2015-10-01

We consider a problem of extrapolating the collision properties of a large polyatomic molecule A-H to make predictions of the dynamical properties for another molecule related to A-H by the substitution of the H atom with a small molecular group X, without explicitly computing the potential energy surface for A-X. We assume that the effect of the -H →-X substitution is embodied in a multidimensional function with unknown parameters characterizing the change of the potential energy surface. We propose to apply the Gaussian Process model to determine the dependence of the dynamical observables on the unknown parameters. This can be used to produce an interval of the observable values which corresponds to physical variations of the potential parameters. We show that the Gaussian Process model combined with classical trajectory calculations can be used to obtain the dependence of the cross sections for collisions of C6H5CN with He on the unknown parameters describing the interaction of the He atom with the CN fragment of the molecule. The unknown parameters are then varied within physically reasonable ranges to produce a prediction uncertainty of the cross sections. The results are normalized to the cross sections for He — C6H6 collisions obtained from quantum scattering calculations in order to provide a prediction interval of the thermally averaged cross sections for collisions of C6H5CN with He.
Kinetics and thermochemistry of polyatomic free radicals: New results and new understandings

NASA Technical Reports Server (NTRS)

Gutman, David; Slagle, Irene R.

1990-01-01

An experimental facility for the study of the chemical kinetics of polyatomic free radicals is described which consists of a heatable tubular reactor coupled to a photoionization mass spectrometer. Its use in different kinds of chemical kinetic studies is also discussed. Examples presented include studies of the C2H3 + O2, C2H3 + HC1, CH3 + O, and CH3 + CH3 reactions. The heat of formation of C2H3 was obtained from the results of the study of the C2H3 + HC1 reaction.
New Cs sputter ion source with polyatomic ion beams for secondary ion mass spectrometry applications

NASA Astrophysics Data System (ADS)

Belykh, S. F.; Palitsin, V. V.; Veryovkin, I. V.; Kovarsky, A. P.; Chang, R. J. H.; Adriaens, A.; Dowsett, M. G.; Adams, F.

2007-08-01

A simple design for a cesium sputter ion source compatible with vacuum and ion-optical systems as well as with electronics of the commercially available Cameca IMS-4f instrument is reported. This ion source has been tested with the cluster primary ions of Sin- and Cun-. Our experiments with surface characterization and depth profiling conducted to date demonstrate improvements of the analytical capabilities of the secondary ion mass spectrometry instrument due to the nonadditive enhancement of secondary ion emission and shorter ion ranges of polyatomic projectiles compared to atomic ones with the same impact energy.
Polyatomic interferences on high precision uranium isotope ratio measurements by MC-ICP-MS: Applications to environmental sampling for nuclear safeguards

DOE PAGES

Pollington, Anthony D.; Kinman, William S.; Hanson, Susan K.; ...

2015-09-04

Modern mass spectrometry and separation techniques have made measurement of major uranium isotope ratios a routine task; however accurate and precise measurement of the minor uranium isotopes remains a challenge as sample size decreases. One particular challenge is the presence of isobaric interferences and their impact on the accuracy of minor isotope 234U and 236U measurements. Furthermore, we present techniques used for routine U isotopic analysis of environmental nuclear safeguards samples and evaluate polyatomic interferences that negatively impact accuracy as well as methods to mitigate their impacts.
A density functional theory based approach for predicting melting points of ionic liquids

DOE PAGES

Chen, Lihua; Bryantsev, Vyacheslav S.

2017-01-17

Accurate prediction of melting points of ILs is important both from the fundamental point of view and from the practical perspective for screening ILs with low melting points and broadening their utilization in a wider temperature range. In this work, we present an ab initio approach to calculating melting points of ILs with known crystal structures and illustrate its application for a series of 11 ILs containing imidazolium/pyrrolidinium cations and halide/polyatomic fluoro-containing anions. The melting point is determined as a temperature at which the Gibbs free energy of fusion is zero. The Gibbs free energy of fusion can be expressedmore » through the use of the Born-Fajans-Haber cycle via the lattice free energy of forming a solid IL from gaseous phase ions and the sum of the solvation free energies of ions comprising IL. Dispersion-corrected density functional theory (DFT) involving (semi)local (PBE-D3) and hybrid exchange-correlation (HSE06-D3) functionals is applied to estimate the lattice enthalpy, entropy, and free energy. The ions solvation free energies are calculated with the SMD-generic-IL solvation model at the M06-2X/6-31+G(d) level of theory under standard conditions. The melting points of ILs computed with the HSE06-D3 functional are in good agreement with the experimental data, with a mean absolute error of 30.5 K and a mean relative error of 8.5%. The model is capable of accurately reproducing the trends in melting points upon variation of alkyl substituents in organic cations and replacement one anion by another. The results verify that the lattice energies of ILs containing polyatomic fluoro-containing anions can be approximated reasonably well using the volume-based thermodynamic approach. However, there is no correlation of the computed lattice energies with molecular volume for ILs containing halide anions. Moreover, entropies of solid ILs follow two different linear relationships with molecular volume for halides and polyatomic fluoro-containing anions. As a result, continuous progress in predicting crystal structures of organic salts with halide anions will be a key factor for successful prediction of melting points with no prior knowledge of the crystal structure.« less

A density functional theory based approach for predicting melting points of ionic liquids

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

Chen, Lihua; Bryantsev, Vyacheslav S.

Accurate prediction of melting points of ILs is important both from the fundamental point of view and from the practical perspective for screening ILs with low melting points and broadening their utilization in a wider temperature range. In this work, we present an ab initio approach to calculating melting points of ILs with known crystal structures and illustrate its application for a series of 11 ILs containing imidazolium/pyrrolidinium cations and halide/polyatomic fluoro-containing anions. The melting point is determined as a temperature at which the Gibbs free energy of fusion is zero. The Gibbs free energy of fusion can be expressedmore » through the use of the Born-Fajans-Haber cycle via the lattice free energy of forming a solid IL from gaseous phase ions and the sum of the solvation free energies of ions comprising IL. Dispersion-corrected density functional theory (DFT) involving (semi)local (PBE-D3) and hybrid exchange-correlation (HSE06-D3) functionals is applied to estimate the lattice enthalpy, entropy, and free energy. The ions solvation free energies are calculated with the SMD-generic-IL solvation model at the M06-2X/6-31+G(d) level of theory under standard conditions. The melting points of ILs computed with the HSE06-D3 functional are in good agreement with the experimental data, with a mean absolute error of 30.5 K and a mean relative error of 8.5%. The model is capable of accurately reproducing the trends in melting points upon variation of alkyl substituents in organic cations and replacement one anion by another. The results verify that the lattice energies of ILs containing polyatomic fluoro-containing anions can be approximated reasonably well using the volume-based thermodynamic approach. However, there is no correlation of the computed lattice energies with molecular volume for ILs containing halide anions. Moreover, entropies of solid ILs follow two different linear relationships with molecular volume for halides and polyatomic fluoro-containing anions. As a result, continuous progress in predicting crystal structures of organic salts with halide anions will be a key factor for successful prediction of melting points with no prior knowledge of the crystal structure.« less
Approximate first-principles anharmonic calculations of polyatomic spectra using MP2 and B3LYP potentials: comparisons with experiment.

PubMed

Roy, Tapta Kanchan; Carrington, Tucker; Gerber, R Benny

2014-08-21

Anharmonic vibrational spectroscopy calculations using MP2 and B3LYP computed potential surfaces are carried out for a series of molecules, and frequencies and intensities are compared with those from experiment. The vibrational self-consistent field with second-order perturbation correction (VSCF-PT2) is used in computing the spectra. The test calculations have been performed for the molecules HNO3, C2H4, C2H4O, H2SO4, CH3COOH, glycine, and alanine. Both MP2 and B3LYP give results in good accord with experimental frequencies, though, on the whole, MP2 gives very slightly better agreement. A statistical analysis of deviations in frequencies from experiment is carried out that gives interesting insights. The most probable percentage deviation from experimental frequencies is about -2% (to the red of the experiment) for B3LYP and +2% (to the blue of the experiment) for MP2. There is a higher probability for relatively large percentage deviations when B3LYP is used. The calculated intensities are also found to be in good accord with experiment, but the percentage deviations are much larger than those for frequencies. The results show that both MP2 and B3LYP potentials, used in VSCF-PT2 calculations, account well for anharmonic effects in the spectroscopy of molecules of the types considered.
Theoretical study of the vibrational relaxation of the methyl radical in collisions with helium

NASA Astrophysics Data System (ADS)

Ma, Qianli; Dagdigian, Paul J.; Alexander, Millard H.

2013-03-01

We report a theoretical investigation of the relaxation of the umbrella vibrational mode (the ν2 mode) of the CH3 molecule in its ground tilde{X}^2A_2^' ' } electronic state in collisions with helium. We have calculated a four-dimensional potential energy surface (PES) for the interaction between CH3 with different umbrella displacements and a helium atom, using a restricted open-shell coupled-cluster method with inclusion of all single, double, and (perturbatively) triple excitations [RCCSD(T)]. With this PES we carried out full close-coupling scattering calculations including all CH3 umbrella-rotational levels with v2 ⩽ 3. To our knowledge, this work represents the first fully quantum calculations of ro-vibrational relaxation of a polyatomic. In more detail, we investigate propensities in the calculated ro-vibrational cross sections and the dependence on initial rotational excitation, as well as determining thermal rate constants. Overall, ro-vibrational relaxation is nearly two orders of magnitude less efficient than pure-rotational relaxation, with a noticeable dependence on the initial rotational level. We predict the room temperature v2 = 1 vibrational relaxation rate constant to be 5.4 × 10-12 cm3 molecule-1 s-1, compared to the rate constants for pure-rotational relaxation of the lower rotational levels (˜2.0 × 10-10 cm3 molecule-1 s-1).
Predicting absorption and dispersion in acoustics by direct simulation Monte Carlo: Quantum and classical models for molecular relaxation.

PubMed

Hanford, Amanda D; O'Connor, Patrick D; Anderson, James B; Long, Lyle N

2008-06-01

In the current study, real gas effects in the propagation of sound waves are simulated using the direct simulation Monte Carlo method for a wide range of frequencies. This particle method allows for treatment of acoustic phenomena at high Knudsen numbers, corresponding to low densities and a high ratio of the molecular mean free path to wavelength. Different methods to model the internal degrees of freedom of diatomic molecules and the exchange of translational, rotational and vibrational energies in collisions are employed in the current simulations of a diatomic gas. One of these methods is the fully classical rigid-rotor/harmonic-oscillator model for rotation and vibration. A second method takes into account the discrete quantum energy levels for vibration with the closely spaced rotational levels classically treated. This method gives a more realistic representation of the internal structure of diatomic and polyatomic molecules. Applications of these methods are investigated in diatomic nitrogen gas in order to study the propagation of sound and its attenuation and dispersion along with their dependence on temperature. With the direct simulation method, significant deviations from continuum predictions are also observed for high Knudsen number flows.
Dynamical tunneling versus fast diffusion for a non-convex Hamiltonian

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

Pittman, S. M.; Tannenbaum, E.; Heller, E. J.

This paper attempts to resolve the issue of the nature of the 0.01-0.1 cm{sup −1} peak splittings observed in high-resolution IR spectra of polyatomic molecules. One hypothesis is that these splittings are caused by dynamical tunneling, a quantum-mechanical phenomenon whereby energy flows between two disconnected regions of phase-space across dynamical barriers. However, a competing classical mechanism for energy flow is Arnol’d diffusion, which connects different regions of phase-space by a resonance network known as the Arnol’d web. The speed of diffusion is bounded by the Nekhoroshev theorem, which guarantees stability on exponentially long time scales if the Hamiltonian is steep.more » Here we consider a non-convex Hamiltonian that contains the characteristics of a molecular Hamiltonian, but does not satisfy the Nekhoroshev theorem. The diffusion along the Arnol’d web is expected to be fast for a non-convex Hamiltonian. While fast diffusion is an unlikely competitor for longtime energy flow in molecules, we show how dynamical tunneling dominates compared to fast diffusion in the nearly integrable regime for a non-convex Hamiltonian, as well as present a new kind of dynamical tunneling.« less
Experimental and Theoretical Studies of Interstellar Grains. Ph.D. Thesis - Maryland Univ., College Park, 1982

NASA Technical Reports Server (NTRS)

Nuth, J. A., III

1981-01-01

Steady state vibrational populations of SiO and CO in dilute black body radiation fields were calculated as a function of total pressure, kinetic temperature and chemical composition of the gas. Approximate calculations for polyatomic molecules are presented. Vibrational disequilibrium becomes increasingly significant as total pressure and radiation density decrease. Many regions of postulated grain formation are found to be far from thermal equilibrium before the onset of nucleation. Calculations based upon classical nucleation theory or equilibrium thermodynamics are expected to be of dubious value in such regions. Laboratory measurements of the extinction of small iron and magnetite grains were made from 195 nm to 830 nm and found to be consistent with predictions based upon published optical constants. This implies that small iron particles are not responsible for the 220 nm interstellar extinction features. Additional measurements are discussed.
Construction of reactive potential energy surfaces with Gaussian process regression: active data selection

NASA Astrophysics Data System (ADS)

Guan, Yafu; Yang, Shuo; Zhang, Dong H.

2018-04-01

Gaussian process regression (GPR) is an efficient non-parametric method for constructing multi-dimensional potential energy surfaces (PESs) for polyatomic molecules. Since not only the posterior mean but also the posterior variance can be easily calculated, GPR provides a well-established model for active learning, through which PESs can be constructed more efficiently and accurately. We propose a strategy of active data selection for the construction of PESs with emphasis on low energy regions. Through three-dimensional (3D) example of H3, the validity of this strategy is verified. The PESs for two prototypically reactive systems, namely, H + H2O ↔ H2 + OH reaction and H + CH4 ↔ H2 + CH3 reaction are reconstructed. Only 920 and 4000 points are assembled to reconstruct these two PESs respectively. The accuracy of the GP PESs is not only tested by energy errors but also validated by quantum scattering calculations.
Interference in acetylene intersystem crossing acts as the molecular analog of Young's double-slit experiment

PubMed Central

de Groot, Mattijs; Field, Robert W.; Buma, Wybren 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). Using high-energy (157-nm) photons from an F2 laser to record excited-state photoelectron spectra, we have decomposed the mixed eigenstates into their S1, T3, T2, and T1 constituent parts. One example of the interpretive power that ensues from the selective sensitivity of the experiment to the individual electronic state characters is the discovery and examination of destructive interference between two doorway-mediated intersystem crossing pathways. This observation of an interference effect in nonradiative decay opens up possibilities for rational coherent control over molecular excited state dynamics. PMID:19179288
DOE Office of Scientific and Technical Information (OSTI.GOV)

Witte, Travis

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 inmore » particulate samples.« less
Some possibilities of using gas mixtures other than air in aerodynamic research

NASA Technical Reports Server (NTRS)

Chapman, Dean R

1956-01-01

A study is made of the advantages that can be realized in compressible-flow research by employing a substitute heavy gas in place of air. The present report is based on the idea that by properly mixing a heavy monatomic gas with a suitable heavy polyatomic gas, it is possible to obtain a heavy gas mixture which has the correct ratio of specific heats and which is nontoxic, nonflammable, thermally stable, chemically inert, and comprised of commercially available components. Calculations were made of wind-tunnel characteristics for 63 gas pairs comprising 21 different polyatomic gases properly mixed with each of three monatomic gases (argon, krypton, and zenon).
Metal-assisted SIMS and cluster ion bombardment for ion yield enhancement

NASA Astrophysics Data System (ADS)

Heile, A.; Lipinsky, D.; Wehbe, N.; Delcorte, A.; Bertrand, P.; Felten, A.; Houssiau, L.; Pireaux, J.-J.; De Mondt, R.; Van Vaeck, L.; Arlinghaus, H. F.

2008-12-01

In addition to structural information, a detailed knowledge of the local chemical environment proves to be of ever greater importance, for example for the development of new types of materials as well as for specific modifications of surfaces and interfaces in multiple fields of materials science or various biomedical and chemical applications. But the ongoing miniaturization and therefore reduction of the amount of material available for analysis constitute a challenge to the detection limits of analytical methods. In the case of time-of-flight secondary ion mass spectrometry (TOF-SIMS), several methods of secondary ion yield enhancement have been proposed. This paper focuses on the investigation of the effects of two of these methods, metal-assisted SIMS and polyatomic primary ion bombardment. For this purpose, thicker layers of polystyrene (PS), both pristine and metallized with different amounts of gold, were analyzed using monoatomic (Ar +, Ga +, Xe +, Bi +) and polyatomic (SF 5+, Bi 3+, C 60+) primary ions. It was found that polyatomic ions generally induce a significant increase of the secondary ion yield. On the other hand, with gold deposition, a yield enhancement can only be detected for monoatomic ion bombardment.
Gaussian process model for extrapolation of scattering observables for complex molecules: From benzene to benzonitrile

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

Cui, Jie; Krems, Roman V.; Li, Zhiying

2015-10-21

We consider a problem of extrapolating the collision properties of a large polyatomic molecule A–H to make predictions of the dynamical properties for another molecule related to A–H by the substitution of the H atom with a small molecular group X, without explicitly computing the potential energy surface for A–X. We assume that the effect of the −H →−X substitution is embodied in a multidimensional function with unknown parameters characterizing the change of the potential energy surface. We propose to apply the Gaussian Process model to determine the dependence of the dynamical observables on the unknown parameters. This can bemore » used to produce an interval of the observable values which corresponds to physical variations of the potential parameters. We show that the Gaussian Process model combined with classical trajectory calculations can be used to obtain the dependence of the cross sections for collisions of C{sub 6}H{sub 5}CN with He on the unknown parameters describing the interaction of the He atom with the CN fragment of the molecule. The unknown parameters are then varied within physically reasonable ranges to produce a prediction uncertainty of the cross sections. The results are normalized to the cross sections for He — C{sub 6}H{sub 6} collisions obtained from quantum scattering calculations in order to provide a prediction interval of the thermally averaged cross sections for collisions of C{sub 6}H{sub 5}CN with He.« less
Ultrafast photochemistry of polyatomic molecules containing labile halogen atoms in solution

NASA Astrophysics Data System (ADS)

Mereshchenko, Andrey S.

Because breaking and making of chemical bonds lies at the heart of chemistry, this thesis focuses on dynamic studies of labile molecules in solutions using ultrafast transient absorption spectroscopy. Specifically, my interest is two-fold: (i) novel reaction intermediates of polyhalogenated carbon, boron and phosphorus compounds; (ii) photophysics and photochemistry of labile copper(II) halide complexes. Excitation of CH2Br2, CHBr3, BBr 3, and PBr3 into n(Br)sigma*(X-Br) states, where X=C, B, or P, leads to direct photoisomerization with formation of isomers having Br-Br bonds as well as rupture of one of X-Br bonds with the formation of a Br atom and a polyatomic radical fragment, which subsequently recombine to form similar isomer products. Nonpolar solvation stabilizes the isomers, consistent with intrinsic reaction coordinate calculations of the isomer ground state potential energy surfaces at the density functional level of theory, and consequently, the involvement of these highly energetic species on chemically-relevant time scales needs to be taken into account. Monochlorocomplexes in methanol solutions promoted to the ligand-to-metal charge transfer (LMCT) excited state predominantly undergo internal conversion via back electron transfer, giving rise to vibrationally hot ground-state parent complexes. Copper-chloride homolitical bond dissociation yielding the solvated copper(I) and Cl- atom/solvent CT complexes constitutes a minor pathway. Insights into ligand substitution mechanisms were acquired by monitoring the recovery of monochloro complexes at the expense of two unexcited dichloro- and unsubstituted forms of Cu(II) complexes also present in the solution. Detailed description of ultrafast excited-state dynamics of CuCl 42- complexes in acetonitrile upon excitation into all possible Ligand Field (LF) excited states and two most intense LMCT transitions is reported. The LF states were found to be nonreactive with lifetimes remarkably longer than those for copper(II) complexes studied so far, in particular, copper blue proteins. The highest 2A1 and lowest 2E LF states relax directly to the ground electronic state whereas the intermediate 2B1 LF state relaxes stepwise through the 2E state. The LMCT excited states are short-lived undergoing either ionic dissociation (CuCl3- + Cl-) or cascading relaxation through the manifold of vibrationally hot LF states to the ground state.
High-Resolution Laser Spectroscopy of Free Radicals in Nearly Degenerate Electronic States

NASA Astrophysics Data System (ADS)

Liu, Jinjun

2017-06-01

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

PubMed

Zheng, Jingjing; Truhlar, Donald G

2012-01-01

Complex molecules often have many structures (conformations) of the reactants and the transition states, and these structures may be connected by coupled-mode torsions and pseudorotations; some but not all structures may have hydrogen bonds in the transition state or reagents. A quantitative theory of the reaction rates of complex molecules must take account of these structures, their coupled-mode nature, their qualitatively different character, and the possibility of merging reaction paths at high temperature. We have recently developed a coupled-mode theory called multi-structural variational transition state theory (MS-VTST) and an extension, called multi-path variational transition state theory (MP-VTST), that includes a treatment of the differences in the multi-dimensional tunneling paths and their contributions to the reaction rate. The MP-VTST method was presented for unimolecular reactions in the original paper and has now been extended to bimolecular reactions. The MS-VTST and MP-VTST formulations of variational transition state theory include multi-faceted configuration-space dividing surfaces to define the variational transition state. They occupy an intermediate position between single-conformation variational transition state theory (VTST), which has been used successfully for small molecules, and ensemble-averaged variational transition state theory (EA-VTST), which has been used successfully for enzyme kinetics. The theories are illustrated and compared here by application to three thermal rate constants for reactions of ethanol with hydroxyl radical--reactions with 4, 6, and 14 saddle points.
Three milieux for interstellar chemistry: gas, dust, and ice

NASA Astrophysics Data System (ADS)

Herbst, Eric

The interdisciplinary science of astrochemistry is 45 years of age, if we pinpoint its origin to have occurred when the first polyatomic molecules were detected in the interstellar gas. Since that time, the field has grown remarkably from an esoteric area of research to one that unites scientists around the globe. Almost 200 different molecules have been detected in the gas-phase of interstellar clouds, mainly by rotational spectroscopy, while dust particles and their icy mantles in colder regions can be probed by vibrational spectroscopy. Astrochemistry is exciting to scientists in a number of different fields. Astronomers are interested in molecular spectra from the heavens because such spectra are excellent probes of the physical conditions where molecules exist, while chemists are interested in the exotic molecules, their spectra, and the unusual chemical processes that produce and destroy them under conditions often very different from those on our home planet. Chemical simulations involving thousands of reactions are now used to calculate concentrations and spectra of interstellar molecules as functions of time. Even biologists share an interest in the subject, because the interstellar clouds of gas and dust, portions of which collapse to form stars and planetary systems, contain organic molecules that may become part of the initial inventory of new planets and may indeed be the precursors of life. An irresistible subject to its practitioners, astrochemistry is proving to be exciting to a much wider audience. In this perspective article, the field is first introduced, and the emphasis is then placed on the three environments in which chemistry occurs in the interstellar medium: the gas phase, the surfaces of bare dust particles, and the ice mantles that cover bare grains in cold dense interstellar clouds. What we do know and what we do not know is distinguished. The status of chemical simulations for a variety of interstellar sources having to do with stellar and planetary evolution is surveyed. An optimistic view of the future of astrochemistry ends the article.
Luminous phenomena and electromagnetic VHF wave emission originated from earthquake-related radon exhalation

NASA Astrophysics Data System (ADS)

Seki, A.; Tobo, I.; Omori, Y.; Muto, J.; Nagahama, H.

2013-12-01

Anomalous luminous phenomena and electromagnetic wave emission before or during earthquakes have been reported (e.g., the 1965 Matsushiro earthquake swarm). However, their mechanism is still unsolved, in spite of many models for these phenomena. Here, we propose a new model about luminous phenomena and electromagnetic wave emission during earthquake by focusing on atmospheric radon (Rn-222) and its daughter nuclides (Po-218 and Po-214). Rn-222, Po-218 and Po-214 are alpha emitters, and these alpha particles ionize atmospheric molecules. A light emission phenomenon, called 'the air luminescence', is caused by de-excitation of the ionized molecules of atmospheric nitrogen due to electron impact ionization from alpha particles. The de-excitation is from the second positive system of neutral nitrogen molecules and the first negative system of nitrogen molecule ion. Wavelengths of lights by these transitions include the visible light wavelength. So based on this mechanism, we proposed a new luminous phenomenon model before or during earthquake: 1. The concentration of atmospheric radon and its daughter nuclides increase anomalously before or during earthquakes, 2. Nitrogen molecules and their ions are excited by alpha particles emitted from Rn-222, Po-218 and Po-214, and air luminescence is generated by their de-excitation. Similarly, electromagnetic VHF wave emission can be explained by ionizing effect of radon and its daughter nuclides. Boyarchuk et al. (2005) proposed a model that electromagnetic VHF wave emission is originated when excited state of neutral clusters changes. Radon gas ionizes atmosphere and forms positively and negatively charged heavy particles. The process of ion hydration in ordinary air can be determined by the formation of complex chemically active structures of the various types of ion radicals. As a result of the association of such hydration radical ions, a neutral cluster, which is dipole quasi-molecules, is formed. A neutral cluster's rotation-rotation transition causes electromagnetic VHF wave emission. We also discuss a possibility of electromagnetic VHF wave emission from excitation of polyatomic molecules by alpha particles from Rn-222 and its daughter nuclides, similar to air luminescence by excitation of nitrogen molecule in the viewpoint of electromagnetic radiation in quantum theory.
Rational extended thermodynamics of a rarefied polyatomic gas with molecular relaxation processes

NASA Astrophysics Data System (ADS)

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.
Kinetic theory of two-temperature polyatomic plasmas

NASA Astrophysics Data System (ADS)

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.
Implementation of polyatomic MCTDHF capability

NASA Astrophysics Data System (ADS)

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.

Identifying the Tunneling Site in Strong-Field Ionization of H_{2}^{+}.

PubMed

Liu, Kunlong; Barth, Ingo

2017-12-15

The tunneling site of the electron in a molecule exposed to a strong laser field determines the initial position of the ionizing electron and, as a result, has a large impact on the subsequent ultrafast electron dynamics on the polyatomic Coulomb potential. Here, the tunneling site of the electron of H_{2}^{+} ionized by a strong circularly polarized (CP) laser pulse is studied by numerically solving the time-dependent Schrödinger equation. We show that the electron removed from the down-field site is directly driven away by the CP field and the lateral photoelectron momentum distribution (LPMD) exhibits a Gaussian-like distribution, whereas the corresponding LPMD of the electron removed from the up-field site differs from the Gaussian shape due to the Coulomb focusing and scattering by the down-field core. Our current study presents the direct evidence clarifying a long-standing controversy over the tunneling site in H_{2}^{+} and raises the important role of the tunneling site in strong-field molecular ionization.
Quantum and classical dynamics of water dissociation on Ni(111): A test of the site-averaging model in dissociative chemisorption of polyatomic molecules

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

Jiang, Bin; Department of Chemical Physics, University of Science and Technology of China, Hefei 230026; Guo, Hua, E-mail: hguo@unm.edu

Recently, we reported the first highly accurate nine-dimensional global potential energy surface (PES) for water interacting with a rigid Ni(111) surface, built on a large number of density functional theory points [B. Jiang and H. Guo, Phys. Rev. Lett. 114, 166101 (2015)]. Here, we investigate site-specific reaction probabilities on this PES using a quasi-seven-dimensional quantum dynamical model. It is shown that the site-specific reactivity is largely controlled by the topography of the PES instead of the barrier height alone, underscoring the importance of multidimensional dynamics. In addition, the full-dimensional dissociation probability is estimated by averaging fixed-site reaction probabilities with appropriatemore » weights. To validate this model and gain insights into the dynamics, additional quasi-classical trajectory calculations in both full and reduced dimensions have also been performed and important dynamical factors such as the steering effect are discussed.« less
The effects of focusing power on TEA CO2 laser-induced gas breakdown and the consequent pulse shaping effects

NASA Astrophysics Data System (ADS)

Beheshtipour, Saleheh; Safari, Ebrahim; Majdabadi, Abbas; Silakhori, Kaveh

2018-02-01

Transversely Excited Atmospheric (TEA) CO2 laser pulses were used in order to generate an optical breakdown in a variety of mono- and polyatomic molecules using different focusing powers. The dependence of the spark kernel geometry and the transmitted pulse shapes on the focusing power as well as the pressure, molecular weight, and ionization energy of the gases was investigated in detail. Partial removal of the transmitted pulse tail in the 0.05-2.6 μs range together with shortened spikes in the 10-60 ns range has been observed by applying a 2.5 cm focal length lens for all the gases. At higher focal lengths, this effect is only incompletely observed for He gas. Spatial-temporal analyses of the laser beams and the relevant plasma plumes indicate that this behavior is due to the drop in the plasma density below the critical level, before the laser pulse tail is completed.
Photophysical behavior of polyatomic molecules

NASA Astrophysics Data System (ADS)

Ware, W. R.

1980-10-01

Part one of this report deals with attempts over the past several years to devise a more sophisticated theory of diffusion controlled reactions than that presented by Collins and Kimball. In particular, the investigators were interested in a more realistic formulation of the problem of high concentration quenching where quenches in the vicinity of the molecular to be quenched must be considered. It was desired however, to obtain a formalism which was tractable mathematically and which contained parameters which would be related to experiment. Part two deals with the photophysics of systems exhibiting molecular association both in the ground and excited states has been studied. The emphasis has been on kinetic models, the measurement of rate constants associated with these models, and the determination of activation parameters and equilibrium thermodynamic parameters associated with the exciplex formation and disappearance. Studies of solvent effects and steric effects on the behavior of exciplex systems have been carried out. The case of rapid equilibrium where the monomer and exciplex decay with the same rate constant has also been examined.
Static time-of-flight secondary ion mass spectrometry analysis of microelectronics related substrates using a polyatomic ion source

NASA Astrophysics Data System (ADS)

Ravanel, X.; Trouiller, C.; Juhel, M.; Wyon, C.; Kwakman, L. F. Tz.; Léonard, D.

2008-12-01

Recent time-of-flight secondary ion mass spectrometry studies using primary ion cluster sources such as Au n+, SF 5+, Bi n+ or C 60+ have shown the great advantages in terms of secondary ion yield enhancement and ion formation efficiency of polyatomic ion sources as compared to monoatomic ion sources like the commonly used Ga +. In this work, the effective gains provided by such a source in the static ToF-SIMS analysis of microelectronics devices were investigated. Firstly, the influence of the number of atoms in the primary cluster ion on secondary ion formation was studied for physically adsorbed di-isononyl phthalate (DNP) (plasticizer) and perfluoropolyether (PFPE). A drastic increase in secondary ion formation efficiency and a much lower detection limit were observed when using a polyatomic primary ion. Moreover, the yield of the higher mass species was much enhanced indicating a lower degree of fragmentation that can be explained by the fact that the primary ion energy is spread out more widely, or that there is a lower energy per incoming ion. Secondly, the influence of the number of Bi atoms in the Bi n primary ion on the information depth was studied using reference thermally grown silicon oxide samples. The information depth provided by a Bi n cluster was shown to be lowered when the number of atoms in the aggregate was increased.
Nicholas Metropolis Award for Outstanding Doctoral Thesis Work in Computational Physics: Quantum many-body physics of ultracold molecules in optical lattices: models and simulation methods

NASA Astrophysics Data System (ADS)

Wall, Michael

2014-03-01

Experimental progress in generating and manipulating synthetic quantum systems, such as ultracold atoms and molecules in optical lattices, has revolutionized our understanding of quantum many-body phenomena and posed new challenges for modern numerical techniques. Ultracold molecules, in particular, feature long-range dipole-dipole interactions and a complex and selectively accessible internal structure of rotational and hyperfine states, leading to many-body models with long range interactions and many internal degrees of freedom. Additionally, the many-body physics of ultracold molecules is often probed far from equilibrium, and so algorithms which simulate quantum many-body dynamics are essential. Numerical methods which are to have significant impact in the design and understanding of such synthetic quantum materials must be able to adapt to a variety of different interactions, physical degrees of freedom, and out-of-equilibrium dynamical protocols. Matrix product state (MPS)-based methods, such as the density-matrix renormalization group (DMRG), have become the de facto standard for strongly interacting low-dimensional systems. Moreover, the flexibility of MPS-based methods makes them ideally suited both to generic, open source implementation as well as to studies of the quantum many-body dynamics of ultracold molecules. After introducing MPSs and variational algorithms using MPSs generally, I will discuss my own research using MPSs for many-body dynamics of long-range interacting systems. In addition, I will describe two open source implementations of MPS-based algorithms in which I was involved, as well as educational materials designed to help undergraduates and graduates perform research in computational quantum many-body physics using a variety of numerical methods including exact diagonalization and static and dynamic variational MPS methods. Finally, I will mention present research on ultracold molecules in optical lattices, such as the exploration of many-body physics with polyatomic molecules, and the next generation of open source matrix product state codes. This work was performed in the research group of Prof. Lincoln D. Carr.
A BGK model for reactive mixtures of polyatomic gases with continuous internal energy

NASA Astrophysics Data System (ADS)

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.
Progress Towards a High-Precision Infrared Spectroscopic Survey of the H_3^+ Ion

NASA Astrophysics Data System (ADS)

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

2015-06-01

The trihydrogen cation, H_3^+, represents one of the most important and fundamental molecular systems. Having only two electrons and three nuclei, H_3^+ is the simplest polyatomic system and is a key testing ground for the development of new techniques for calculating potential energy surfaces and predicting molecular spectra. Corrections that go beyond the Born-Oppenheimer approximation, including adiabatic, non-adiabatic, relativistic, and quantum electrodynamic corrections are becoming more feasible to calculate. As a result, experimental measurements performed on the H_3^+ ion serve as important benchmarks which are used to test the predictive power of new computational methods. By measuring many infrared transitions with precision at the sub-MHz level it is possible to construct a list of the most highly precise experimental rovibrational energy levels for this molecule. Until recently, only a select handful of infrared transitions of this molecule have been measured with high precision (˜ 1 MHz). Using the technique of Noise Immune Cavity Enhanced Optical Heterodyne Velocity Modulation Spectroscopy, we are aiming to produce the largest high-precision spectroscopic dataset for this molecule to date. Presented here are the current results from our survey along with a discussion of the combination differences analysis used to extract the experimentally determined rovibrational energy levels. O. Polyansky, et al., Phil. Trans. R. Soc. A (2012), 370, 5014. M. Pavanello, et al., J. Chem. Phys. (2012), 136, 184303. L. Diniz, et al., Phys. Rev. A (2013), 88, 032506. L. Lodi, et al., Phys. Rev. A (2014), 89, 032505. J. Hodges, et al., J. Chem. Phys (2013), 139, 164201.
Prebiotic chemical evolution in the astrophysical context.

PubMed

Ziurys, L M; Adande, G R; Edwards, J L; Schmidt, D R; Halfen, D T; Woolf, N J

2015-06-01

An ever increasing amount of molecular material is being discovered in the interstellar medium, associated with the birth and death of stars and planetary systems. Radio and millimeter-wave astronomical observations, made possible by high-resolution laboratory spectroscopy, uniquely trace the history of gas-phase molecules with biogenic elements. Using a combination of both disciplines, the full extent of the cycling of molecular matter, from circumstellar ejecta of dying stars - objects which expel large amounts of carbon - to nascent solar systems, has been investigated. Such stellar ejecta have been found to exhibit a rich and varied chemical content. Observations demonstrate that this molecular material is passed onto planetary nebulae, the final phase of stellar evolution. Here the star sheds almost its entire original mass, becoming an ultraviolet-emitting white dwarf. Molecules such as H2CO, HCN, HCO(+), and CCH are present in significant concentrations across the entire age span of such nebulae. These data suggest that gas-phase polyatomic, carbon-containing molecules survive the planetary nebula phase and subsequently are transported into the interstellar medium, seeding the chemistry of diffuse and then dense clouds. The extent of the chemical complexity in dense clouds is unknown, hindered by the high spectral line density. Organic species such as acetamide and methyl amine are present in such objects, and NH2CHO has a wide Galactic distribution. However, organophosphorus compounds have not yet been detected in dense clouds. Based on carbon and nitrogen isotope ratios, molecular material from the ISM appears to become incorporated into solar system planetesimals. It is therefore likely that interstellar synthesis influences prebiotic chemistry on planet surfaces.
Constructing polyatomic potential energy surfaces by interpolating diabatic Hamiltonian matrices with demonstration on green fluorescent protein chromophore

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

Park, Jae Woo; Rhee, Young Min, E-mail: ymrhee@postech.ac.kr; Department of Chemistry, Pohang University of Science and Technology

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 diabaticmore » 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.« less
Doppler Broadening Thermometry Based on Cavity Ring-Down Spectroscopy

NASA Astrophysics Data System (ADS)

Wang, Jin; Sun, Yu Robert; Cheng, Cunfeng; Tao, Lei-Gang; Tan, Yan; Kang, Peng; Liu, An-Wen; Hu, Shui-Ming

2016-06-01

A Doppler broadening thermometry (DBT) instrument is implemented based on a laser-locked cavity ring-down spectrometer. [1,2] It can be used to determine the Boltzmann constant by measuring the Doppler width of a molecular ro-vibrational transition in the near infrared. Compared with conventional direct absorption methods, the high-sensitivity of CRDS allows to reach satisfied precision at lower sample pressures, which reduces the influence due to collisions. By measuring the ro-vibrational transition of C_2H_2 at 787 nm, we demonstrate a statistical uncertainty of 6 ppm (part per million) in the determined linewidth by several hours' measurement at a sample pressure of 1.5 Pa. [3] However, the complicity in the spectrum of a polyatomic molecule induces potential systematic influence on the line profile due to nearby ``hidden'' lines from weak bands or minor isotopologues. Recently, the instrument has been upgraded in both sensitivity and frequency accuracy. A narrow-band fiber laser frequency-locked to a frequency comb is applied, and overtone transitions at 1.56 μm of the 12C16O molecule are used in the CRDS-DBT measurements. The simplicity of the spectrum of the diatomic CO molecule eliminates the potential influence from ``hidden'' lines. Our preliminary measurements and analysis show that it is feasible to pursue a DBT measurement toward the 1 ppm precision. H. Pan, et al., Rev. Sci. Instrum. 82, 103110 (2011) Y. R. Sun, et al., Opt. Expr., 19, 19993 (2011) C.-F. Cheng, et al., Metrologia, 52, S385 (2015)
Linear electric field time-of-flight ion mass spectrometer

DOEpatents

Funsten, Herbert O [Los Alamos, NM; Feldman, William C [Los Alamos, NM

2008-06-10

A linear electric field ion mass spectrometer having an evacuated enclosure with means for generating a linear electric field located in the evacuated enclosure and means for injecting a sample material into the linear electric field. A source of pulsed ionizing radiation injects ionizing radiation into the linear electric field to ionize atoms or molecules of the sample material, and timing means determine the time elapsed between ionization of atoms or molecules and arrival of an ion out of the ionized atoms or molecules at a predetermined position.
Photoelectron wave function in photoionization: plane wave or Coulomb wave?

PubMed

Gozem, Samer; Gunina, Anastasia O; Ichino, Takatoshi; Osborn, David L; Stanton, John F; Krylov, Anna I

2015-11-19

The calculation of absolute total cross sections requires accurate wave functions of the photoelectron and of the initial and final states of the system. The essential information contained in the latter two can be condensed into a Dyson orbital. We employ correlated Dyson orbitals and test approximate treatments of the photoelectron wave function, that is, plane and Coulomb waves, by comparing computed and experimental photoionization and photodetachment spectra. We find that in anions, a plane wave treatment of the photoelectron provides a good description of photodetachment spectra. For photoionization of neutral atoms or molecules with one heavy atom, the photoelectron wave function must be treated as a Coulomb wave to account for the interaction of the photoelectron with the +1 charge of the ionized core. For larger molecules, the best agreement with experiment is often achieved by using a Coulomb wave with a partial (effective) charge smaller than unity. This likely derives from the fact that the effective charge at the centroid of the Dyson orbital, which serves as the origin of the spherical wave expansion, is smaller than the total charge of a polyatomic cation. The results suggest that accurate molecular photoionization cross sections can be computed with a modified central potential model that accounts for the nonspherical charge distribution of the core by adjusting the charge in the center of the expansion.
Ab Initio Potential Energy Surfaces and Quantum Dynamics for Polyatomic Bimolecular Reactions.

PubMed

Fu, Bina; Zhang, Dong H

2018-05-08

There has been great progress in the development of potential energy surfaces (PESs) and quantum dynamics calculations in the gas phase. The establishment of a fitting procedure for highly accurate PESs and new developments in quantum reactive scattering on reliable PESs allow accurate characterization of reaction dynamics beyond triatomic systems. This review will give the recent development in our group in constructing ab initio PESs based on neural networks and the time-dependent wave packet calculations for bimolecular reactions beyond three atoms. Bimolecular reactions of current interest to the community, namely, OH + H 2 , H + H 2 O, OH + CO, H + CH 4 , and Cl + CH 4 , are focused on. Quantum mechanical characterization of these reactions uncovers interesting dynamical phenomena with an unprecedented level of sophistication and has greatly advanced our understanding of polyatomic reaction dynamics.
Molecular ion yield enhancement induced by gold deposition in static secondary ion mass spectrometry

NASA Astrophysics Data System (ADS)

Wehbe, Nimer; Delcorte, Arnaud; Heile, Andreas; Arlinghaus, Heinrich F.; Bertrand, Patrick

2008-12-01

Static ToF-SIMS was used to evaluate the effect of gold condensation as a sample treatment prior to analysis. The experiments were carried out with a model molecular layer (Triacontane M = 422.4 Da), upon atomic (In +) and polyatomic (Bi 3+) projectile bombardment. The results indicate that the effect of molecular ion yield improvement using gold metallization exists only under atomic projectile impact. While the quasi-molecular ion (M+Au) + signal can become two orders of magnitude larger than that of the deprotonated molecular ion from the pristine sample under In + bombardment, it barely reaches the initial intensity of (M-H) + when Bi 3+ projectiles are used. The differences observed for mono- and polyatomic primary ion bombardment might be explained by differences in near-surface energy deposition, which influences the sputtering and ionization processes.
Shock wave structure in rarefied polyatomic gases with large relaxation time for the dynamic pressure

NASA Astrophysics Data System (ADS)

Taniguchi, Shigeru; Arima, Takashi; Ruggeri, Tommaso; Sugiyama, Masaru

2018-05-01

The shock wave structure in rarefied polyatomic gases is analyzed based on extended thermodynamics (ET). In particular, the case with large relaxation time for the dynamic pressure, which corresponds to large bulk viscosity, is considered by adopting the simplest version of extended thermodynamics with only 6 independent fields (ET6); the mass density, the velocity, the temperature and the dynamic pressure. Recently, the validity of the theoretical predictions by ET was confirmed by the numerical analysis based on the kinetic theory in [S Kosuge and K Aoki: Phys. Rev. Fluids, Vol. 3, 023401 (2018)]. It was shown that numerical results using the polyatomic version of ellipsoidal statistical model agree with the theoretical predictions by ET for small or moderately large Mach numbers. In the present paper, first, we compare the theoretical predictions by ET6 with the ones by kinetic theory for large Mach number under the same assumptions, that is, the gas is polytropic and the bulk viscosity is proportional to the temperature. Second, the shock wave structure for large Mach number in a non-polytropic gas is analyzed with the particular interest in the effect of the temperature dependence of specific heat and the bulk viscosity on the shock wave structure. Through the analysis of the case of a rarefied carbon dioxide (CO2) gas, it is shown that these temperature dependences play important roles in the precise analysis of the structure for strong shock waves.
Superradiance Effects in the Linear and Nonlinear Optical Response of Quantum Dot Molecules

NASA Astrophysics Data System (ADS)

Sitek, A.; Machnikowski, P.

2008-11-01

We calculate the linear optical response from a single quantum dot molecule and the nonlinear, four-wave-mixing response from an inhomogeneously broadened ensemble of such molecules. We show that both optical signals are affected by the coupling-dependent superradiance effect and by optical interference between the two polarizations. As a result, the linear and nonlinear responses are not identical.
A Separable Insertion Method to Calculate Atomic and Molecular Resonances on a FE-DVR Grid using Exterior Complex Scaling

NASA Astrophysics Data System (ADS)

Abeln, Brant Anthony

The study of metastable electronic resonances, anion or neutral states of finite lifetime, in molecules is an important area of research where currently no theoretical technique is generally applicable. The role of theory is to calculate both the position and width, which is proportional to the inverse of the lifetime, of these resonances and how they vary with respect to nuclear geometry in order to generate potential energy surfaces. These surfaces are the basis of time-dependent models of the molecular dynamics where the system moves towards vibrational excitation or fragmentation. Three fundamental electronic processes that can be modeled this way are dissociative electronic attachment, vibrational excitation through electronic impact and autoionization. Currently, experimental investigation into these processes is being preformed on polyatomic molecules while theoreticians continue their fifty-year-old search for robust methods to calculate them. The separable insertion method, investigated in this thesis, seeks to tackle the problem of calculating metastable resonances by using existing quantum chemistry tools along with a grid-based method employing exterior complex scaling (ECS). Modern quantum chemistry methods are extremely efficient at calculating ground and (bound) excited electronic states of atoms and molecules by utilizing Gaussian basis functions. These functions provide both a numerically fast and analytic solution to the necessary two-electron, six-dimensional integrals required in structure calculations. However, these computer programs, based on analytic Gaussian basis sets, cannot construct solutions that are not square-integrable, such as resonance wavefunctions. ECS, on the other hand, can formally calculate resonance solutions by rotating the asymptotic electronic coordinates into the complex plane. The complex Siegert energies for resonances, Eres = ER - iGamma/2 where ER is the real-valued position of the resonance and Gamma is the width of the resonance, can be found directly as an isolated pole in the complex energy plane. Unlike the straight complex scaling, ECS on the electronic coordinates overcomes the non-analytic behavior of the nuclear attraction potential, as a function of complex [special characters omitted] where the sum is over each nucleus in a molecular system. Discouragingly, the Gaussian basis functions, which are computationally well-suited for bound electronic structure, fail at forming an effective basis set for ECS due to the derivative discontinuity generated by the complex coordinate rotation and the piecewise defined contour. This thesis seeks to explore methods for implementing ECS indirectly without losing the numerical simplicity and power of Gaussian basis sets. The separable insertion method takes advantage of existing software by constructing a N2-term separable potential of the target system using Gaussian functions to be inserted into a finite-element discrete variable representation (FE-DVR) grid that implements ECS. This work reports an exhaustive investigation into this approach for calculating resonances. This thesis shows that this technique is successful at describing an anion shape resonance of a closed-shell atom or molecule in the static-exchange approximation. This method is applied to the 2P Be-, 2pig N2- and 2pi u CO2- shape resonances to calculate their complex Seigert energies. Additionally, many details on the exact construction of the separable potential and of the expansion basis are explored. The future work considers methods for faster convergence of the resonance energy, moving beyond the static-exchange approximation and applying this technique to polyatomic systems of interest.
Thermomagnetic torques in polyatomic gases

NASA Technical Reports Server (NTRS)

Hildebrandt, A. F.; Wood, C. T.

1972-01-01

The application of the Scott effect to the dynamics of galactic and stellar rotation is investigated. Efforts were also made to improve the sensitivity and stability of torque measurements and understand the microscopic mechanism that causes the Scott effect.
Peculiarities of high-overtone transition probabilities in carbon monoxide revealed by high-precision calculation

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

Medvedev, Emile S., E-mail: esmedved@orc.ru; Meshkov, Vladimir V.; Stolyarov, Andrey V.

In the recent work devoted to the calculation of the rovibrational line list of the CO molecule [G. Li et al., Astrophys. J., Suppl. Ser. 216, 15 (2015)], rigorous validation of the calculated parameters including intensities was carried out. In particular, the Normal Intensity Distribution Law (NIDL) [E. S. Medvedev, J. Chem. Phys. 137, 174307 (2012)] was employed for the validation purposes, and it was found that, in the original CO line list calculated for large changes of the vibrational quantum number up to Δn = 41, intensities with Δn > 11 were unphysical. Therefore, very high overtone transitions weremore » removed from the published list in Li et al. Here, we show how this type of validation is carried out and prove that the quadruple precision is indispensably required to predict the reliable intensities using the conventional 32-bit computers. Based on these calculations, the NIDL is shown to hold up for the 0 → n transitions till the dissociation limit around n = 83, covering 45 orders of magnitude in the intensity. The low-intensity 0 → n transition predicted in the work of Medvedev [Determination of a new molecular constant for diatomic systems. Normal intensity distribution law for overtone spectra of diatomic and polyatomic molecules and anomalies in overtone absorption spectra of diatomic molecules, Institute of Chemical Physics, Russian Academy of Sciences, Chernogolovka, 1984] at n = 5 is confirmed, and two additional “abnormal” intensities are found at n = 14 and 23. Criteria for the appearance of such “anomalies” are formulated. The results could be useful to revise the high-overtone molecular transition probabilities provided in spectroscopic databases.« less

Prospects for P-bearing molecules in cometary atmospheres

NASA Astrophysics Data System (ADS)

Boice, Daniel; de Almeida, Amaury

Phosphorus is a key element in all known forms of life and phosphorus-bearing compounds have been observed in space. Phosphorus is ubiquitous in meteorites, albeit in small quantities, with phosphates being found in stoney meteorites and phosphides have been identified in iron meteorites. It has been detected as part of the dust component in comet Halley but searches for P-bearing species in the gas phase in comets have been unsuccessful. Based of its moderate cosmic abundance (eighteenth most abundant element, [P]/[N] = 4 x 10-3 ) and the positive identification of P-bearing species in the interstellar medium (such as, PN, PC, HCP and PO), we would expect simple molecules, diatomics (like PH, PO, PC, PS), triatomics (like HCP and PH2 ), and possibly other polyatomics (like phosphine PH3 and diphosphine P2 H4 ), to exist in cometary ices, hence released into the gas phase upon ice sublimation. Our fluid dynamics model with chemistry of cometary comae (SUISEI) has been adapted to study this problem. SUISEI produces cometocentric abundances of the coma gas species; velocities of the bulk gas, light atomic and molecular hydrogen with escape, and electrons; gas and electron temperatures; column densities to facilitate comparison with observations; coma energy budget quantities; attenuation of the solar irradiance; and other quantities that can be related readily to observations. We present results from the first quantitative study of phosphorus-bearing molecules in comets to identify likely species containing phosphorus to aid in future searches for this important element in comets, possibly shedding light on issues of comet formation (time and place) and matters of the prebiotic to biotic evolution of life. Acknowledgements. This work was supported by the NSF Planetary Astronomy Program.
Characteristics of energy exchange between inter- and intramolecular degrees of freedom in crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) with implications for coarse-grained simulations of shock waves in polyatomic molecular crystals

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

Kroonblawd, Matthew P.; Sewell, Thomas D., E-mail: sewellt@missouri.edu; Maillet, Jean-Bernard, E-mail: jean-bernard.maillet@cea.fr

2016-02-14

In this report, we characterize the kinetics and dynamics of energy exchange between intramolecular and intermolecular degrees of freedom (DoF) in crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). All-atom molecular dynamics (MD) simulations are used to obtain predictions for relaxation from certain limiting initial distributions of energy between the intra- and intermolecular DoF. The results are used to parameterize a coarse-grained Dissipative Particle Dynamics at constant Energy (DPDE) model for TATB. Each TATB molecule in the DPDE model is represented as an all-atom, rigid-molecule mesoparticle, with explicit external (molecular translational and rotational) DoF and coarse-grained implicit internal (vibrational) DoF. In addition to conserving linearmore » and angular momentum, the DPDE equations of motion conserve the total system energy provided that particles can exchange energy between their external and internal DoF. The internal temperature of a TATB molecule is calculated using an internal equation of state, which we develop here, and the temperatures of the external and internal DoF are coupled using a fluctuation-dissipation relation. The DPDE force expression requires specification of the input parameter σ that determines the rate at which energy is exchanged between external and internal DoF. We adjusted σ based on the predictions for relaxation processes obtained from MD simulations. The parameterized DPDE model was employed in large-scale simulations of shock compression of TATB. We show that the rate of energy exchange governed by σ can significantly influence the transient behavior of the system behind the shock.« less
Characterising molecules for fundamental physics: an accurate spectroscopic model of methyltrioxorhenium derived from new infrared and millimetre-wave measurements.

PubMed

Asselin, Pierre; Berger, Yann; Huet, Thérèse R; Margulès, Laurent; Motiyenko, Roman; Hendricks, Richard J; Tarbutt, Michael R; Tokunaga, Sean K; Darquié, Benoît

2017-02-08

Precise spectroscopic analysis of polyatomic molecules enables many striking advances in physical chemistry and fundamental physics. We use several new high-resolution spectroscopic devices to improve our understanding of the rotational and rovibrational structure of methyltrioxorhenium (MTO), the achiral parent of a family of large oxorhenium compounds that are ideal candidate species for a planned measurement of parity violation in chiral molecules. Using millimetre-wave and infrared spectroscopy in a pulsed supersonic jet, a cryogenic buffer gas cell, and room temperature absorption cells, we probe the ground state and the Re[double bond, length as m-dash]O antisymmetric and symmetric stretching excited states of both CH 3 187 ReO 3 and CH 3 185 ReO 3 isotopologues in the gas phase with unprecedented precision. By extending the rotational spectra to the 150-300 GHz range, we characterize the ground state rotational and hyperfine structure up to J = 43 and K = 41, resulting in refinements to the rotational, quartic and hyperfine parameters, and the determination of sextic parameters and a centrifugal distortion correction to the quadrupolar hyperfine constant. We obtain rovibrational data for temperatures between 6 and 300 K in the 970-1015 cm -1 range, at resolutions down to 8 MHz and accuracies of 30 MHz. We use these data to determine more precise excited-state rotational, Coriolis and quartic parameters, as well as the ground-state centrifugal distortion parameter D K of the 187 Re isotopologue. We also account for hyperfine structure in the rovibrational transitions and hence determine the upper state rhenium atom quadrupole coupling constant eQq'.
Monoatomic and cluster beam effect on ToF-SIMS spectra of self-assembled monolayers on gold

NASA Astrophysics Data System (ADS)

Tuccitto, N.; Torrisi, V.; Delfanti, I.; Licciardello, A.

2008-12-01

Self-assembled monolayers represent well-defined systems that is a good model surface to study the effect of primary ion beams used in secondary ion mass spectrometry. The effect of polyatomic primary beams on both aliphatic and aromatic self-assembled monolayers has been studied. In particular, we analysed the variation of the relative secondary ion yield of both substrate metal-cluster (Au n-) in comparison with the molecular ions (M -) and clusters (M xAu y-) by using Bi +, Bi 3+, Bi 5+ beams. Moreover, the differences in the secondary ion generation efficiency are discussed. The main effect of the cluster beams is related to an increased formation of low-mass fragments and to the enhancement of the substrate related gold-clusters. The results show that, at variance of many other cases, the static SIMS of self-assembled monolayers does not benefit of the use of polyatomic primary ions.
Quantum monodromy and quantum phase transitions in floppy molecules

NASA Astrophysics Data System (ADS)

Larese, Danielle

2012-10-01

A simple algebraic Hamiltonian has been used to explore the vibrational and rotational spectra of the skeletal bending modes of HCNO, BrCNO, NCNCS, and other "floppy" (quasi-linear or quasi-bent) molecules. These molecules have large-amplitude, low-energy bending modes and champagne-bottle potential surfaces, making them good candidates for observing quantum phase transitions (QPT). We describe the geometric phase transitions from bent to linear in these and other non-rigid molecules, quantitatively analyzing the spectroscopic signatures of ground state QPT, excited state QPT, and quantum monodromy. The algebraic framework is ideal for this work because of its small calculational effort yet robust results. Although these methods have historically found success with tri-and four-atomic molecules, we now address five-atomic and simple branched molecules such as CH3NCO and GeH3NCO. Extraction of potential functions are completed for several molecules, resulting in predictions of barriers to linearity and equilibrium bond angles.
Ab initio quantum direct dynamics simulations of ultrafast photochemistry with Multiconfigurational Ehrenfest approach

NASA Astrophysics Data System (ADS)

Makhov, Dmitry V.; Symonds, Christopher; Fernandez-Alberti, Sebastian; Shalashilin, Dmitrii V.

2017-08-01

The Multiconfigurational Ehrenfest (MCE) method is a quantum dynamics technique which allows treatment of a large number of quantum nuclear degrees of freedom. This paper presents a review of MCE and its recent applications, providing a summary of the formalisms, including its ab initio direct dynamics versions and also giving a summary of recent results. Firstly, we describe the Multiconfigurational Ehrenfest version 2 (MCEv2) method and its applicability to direct dynamics and report new calculations which show that the approach converges to the exact result in model systems with tens of degrees of freedom. Secondly, we review previous ;on the fly; ab initio Multiple Cloning (AIMC-MCE) MCE dynamics results obtained for systems of a similar size, in which the calculations treat every electron and every nucleus of a polyatomic molecule on a fully quantum basis. We also review the Time Dependent Diabatic Basis (TDDB) version of the technique and give an example of its application. We summarise the details of the sampling techniques and interpolations used for calculation of the matrix elements, which make our approach efficient. Future directions of work are outlined.
Physical explanation of the periodic table.

PubMed

Ostrovsky, V N

2003-05-01

The Periodic Table of the elements, the most important generalization in chemistry, is often considered as a representative special case in the study of the relation between chemistry and physics. Its quantum interpretation was initiated, but not completed, by Niels Bohr. In this paper, post-Bohr conceptual developments are discussed from historical and epistemological points of view. The difference between high-precision numerical calculations for individual atoms and the theory of the periodic system as a whole is emphasized. Periodic laws met in Nature are not restricted to the chemical Periodic Table. A comparative study of these laws makes it possible to single out essential features that define the particular pattern of periodicity. It is shown that the periodic system of neutral ground state atoms now has a firm nonempirical quantum-theoretical basis. Alternative approaches, based on group theory and other mathematical schemes, are briefly discussed. It is argued that, while quantum theory is capable of fully accurate calculations for relatively simple atoms or molecular objects, the complexity of polyatomic molecules and chemical reactions guarantees the flourishing of chemistry as a separate scientific discipline.
Picosecond coherent anti-Stokes Raman scattering (CARS) study of vibrational dephasing of carbon disulfide and benzene in solution

NASA Technical Reports Server (NTRS)

Perry, Joseph W.; Woodward, Anne M.; Stephenson, John C.

1986-01-01

The vibrational dephasing of the 656/cm mode (nu1, a1g) of CS2 and the 991/cm mode (nu2, a1g) of benzene have been studied as a function of concentration in mixtures with a number of solvents using a ps time-resolved CARS technique. This technique employs two tunable synchronously-pumped mode-locked dye lasers in a stimulated Raman pump, coherent anti-Stokes Raman probe time-resolved experiment. Results are obtained for CS2 in carbon tetrachloride, benzene, nitrobenzene, and ethanol and for benzene nu2 in CS2. The dephasing rates of CS2 nu1 increase on dilution with the polar solvents and decrease or remain constant on dilution with the nonpolar solvents. The CS2/benzene solutions show a contrasting behavior, with the CS2 nu1 dephasing rate being nearly independent of concentration whereas the benzene nu2 dephasing rate decreases on dilution. These results are compared to theoretical models for vibrational dephasing of polyatomic molecules in solution.
Hyperconjugation in the S1 State of Substituted Toluene Probed by Infrared Spectroscopy

NASA Astrophysics Data System (ADS)

Chiba, Takashi; Okuyama, Katsuhiko; Fujii, Asuka

2016-06-01

Internal rotation of the methyl group in substituted toluenes is one of prototypes of large amplitude motions in polyatomic molecules. The internal rotation of o-fluorotoluene is strongly hindered in the S0 state, but that of m-fluorotoluene is almost free. For the S1 state, however, the substantial changes of the internal rotation potentials have been reported; while the potential barrier in the o-isomer drastically decreases and the methyl group becomes almost a free rotor, the barrier in the m-isomer largely increases. These surprising barrier changes have been attributed to the methyl conformation-dependent stabilization in the S1 state by the π*-σ* hyperconjugation. In the present study, to test this interpretation, we observed infrared spectra of o- and m-fluorotoluenes in the S0 and S1 states. Both the isomers showed decrease of the methyl CH stretch frequencies upon the electronic excitation. We concluded that this frequency decrease is the evidence of the π*-σ* hyperconjugation. K,Okuyama.;N,Mikami.;M,Ito. J.Phys.Chem. 1985, 89, 5617 H,Nakai.;M,Kawai. Chem.Phys.Lett 1999, 307, 272
On the Mass of Atoms in Molecules: Beyond the Born-Oppenheimer Approximation

NASA Astrophysics Data System (ADS)

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 computation of high-precision molecular spectra.
Electron Scattering Studies of Gas Phase Molecular Structure at High Temperature

NASA Astrophysics Data System (ADS)

Mawhorter, Richard J., Jr.

A high precision counting electron diffraction study of the structure of gaseous sulfur dioxide as a function of temperature from 300(DEGREES) to 1000(DEGREES)K is presented. The results agree well with current theory, and yield insight into the effects of anharmonicity on molecular structure. Another aspect of molecular structure is the molecular charge density distribution. The difference (DELTA)(sigma) is between the electron scattering cross sections for the actual molecule and independent atom model (IAM) are a sensitive measure of the change in this distribution due to bond formation. These difference cross sections have been calculated using ab initio methods, and the results for a wide range of simple polyatomic molecules are presented. Such calculations are routinely done for a single, fixed molecular geometry, an approach which neglects the effects of the vibrational motion of real molecules. The effect of vibrational averaging is studied in detail for the three normal vibrational modes of H(,2)O in the ground state. The effects are small, lending credence to the practice of comparing cross sections calculated at a fixed geometry with inherently averaged experimental data. The efficacy of the standard formula used to account for vibrational averaging in the IAM is also examined. Finally, the nature of the ionic bond is probed with an experimental study of the structure of alkali chlorides, NaCl, KCl, RbCl, and CsCl, in the gas phase. Temperatures from 840-960(DEGREES)K were required to achieve the necessary vapor pressures of approximately 0.01 torr. A planar rhombic structure for the dimer molecule is confirmed, with a fairly uniform decrease of the chlorine-alkali-chlorine angle as the alkalis increase in size. The experiment also yields information on the amount of dimer present in the vapor, and these results are compared with thermodynamic values.
Fastest Formation Routes of Nanocarbons in Solution Plasma Processes.

PubMed

Morishita, Tetsunori; Ueno, Tomonaga; Panomsuwan, Gasidit; Hieda, Junko; Yoshida, Akihito; Bratescu, Maria Antoaneta; Saito, Nagahiro

2016-11-14

Although solution-plasma processing enables room-temperature synthesis of nanocarbons, the underlying mechanisms are not well understood. We investigated the routes of solution-plasma-induced nanocarbon formation from hexane, hexadecane, cyclohexane, and benzene. The synthesis rate from benzene was the highest. However, the nanocarbons from linear molecules were more crystalline than those from ring molecules. Linear molecules decomposed into shorter olefins, whereas ring molecules were reconstructed in the plasma. In the saturated ring molecules, C-H dissociation proceeded, followed by conversion into unsaturated ring molecules. However, unsaturated ring molecules were directly polymerized through cation radicals, such as benzene radical cation, and were converted into two- and three-ring molecules at the plasma-solution interface. The nanocarbons from linear molecules were synthesized in plasma from small molecules such as C 2 under heat; the obtained products were the same as those obtained via pyrolysis synthesis. Conversely, the nanocarbons obtained from ring molecules were directly synthesized through an intermediate, such as benzene radical cation, at the interface between plasma and solution, resulting in the same products as those obtained via polymerization. These two different reaction fields provide a reasonable explanation for the fastest synthesis rate observed in the case of benzene.
Fastest Formation Routes of Nanocarbons in Solution Plasma Processes

PubMed Central

Morishita, Tetsunori; Ueno, Tomonaga; Panomsuwan, Gasidit; Hieda, Junko; Yoshida, Akihito; Bratescu, Maria Antoaneta; Saito, Nagahiro

2016-01-01

Although solution-plasma processing enables room-temperature synthesis of nanocarbons, the underlying mechanisms are not well understood. We investigated the routes of solution-plasma-induced nanocarbon formation from hexane, hexadecane, cyclohexane, and benzene. The synthesis rate from benzene was the highest. However, the nanocarbons from linear molecules were more crystalline than those from ring molecules. Linear molecules decomposed into shorter olefins, whereas ring molecules were reconstructed in the plasma. In the saturated ring molecules, C–H dissociation proceeded, followed by conversion into unsaturated ring molecules. However, unsaturated ring molecules were directly polymerized through cation radicals, such as benzene radical cation, and were converted into two- and three-ring molecules at the plasma–solution interface. The nanocarbons from linear molecules were synthesized in plasma from small molecules such as C2 under heat; the obtained products were the same as those obtained via pyrolysis synthesis. Conversely, the nanocarbons obtained from ring molecules were directly synthesized through an intermediate, such as benzene radical cation, at the interface between plasma and solution, resulting in the same products as those obtained via polymerization. These two different reaction fields provide a reasonable explanation for the fastest synthesis rate observed in the case of benzene. PMID:27841288
Mass Dependency of Isotope Fractionation of Gases Under Thermal Gradient and Its Possible Implications for Planetary Atmosphere Escaping Process

NASA Technical Reports Server (NTRS)

Sun, Tao; Niles, Paul; Bao, Huiming; Socki, Richard

2014-01-01

Physical processes that unmix elements/isotopes of gas molecules involve phase changes, diffusion (chemical or thermal), effusion and gravitational settling. Some of those play significant roles for the evolution of chemical and isotopic compositions of gases in planetary bodies which lead to better understanding of surface paleoclimatic conditions, e.g. gas bubbles in Antarctic ice, and planetary evolution, e.g. the solar-wind erosion induced gas escaping from exosphere on terrestrial planets.. A mass dependent relationship is always expected for the kinetic isotope fractionations during these simple physical processes, according to the kinetic theory of gases by Chapman, Enskog and others [3-5]. For O-bearing (O16, -O17, -O18) molecules the alpha O-17/ alpha O-18 is expected at 0.5 to 0.515, and for S-bearing (S32,-S33. -S34, -S36) molecules, the alpha S-33/ alpha S-34 is expected at 0.5 to 0.508, where alpha is the isotope fractionation factor associated with unmixing processes. Thus, one isotope pair is generally proxied to yield all the information for the physical history of the gases. However, we recently] reported the violation of mass law for isotope fractionation among isotope pairs of multiple isotope system during gas diffusion or convection under thermal gradient (Thermal Gradient Induced Non-Mass Dependent effect, TGI-NMD). The mechanism(s) that is responsible to such striking observation remains unanswered. In our past studies, we investigated polyatomic molecules, O2 and SF6, and we suggested that nuclear spin effect could be responsible to the observed NMD effect in a way of changing diffusion coefficients of certain molecules, owing to the fact of negligible delta S-36 anomaly for SF6.. On the other hand, our results also showed that for both diffusion and convection under thermal gradient, this NMD effect is increased by lower gas pressure, bigger temperature gradient and lower average temperature, which indicate that the nuclear spin effect may not be the significant contributor as the energies involved in the hyperfine effect are much smaller than those with molecular collisions, especially under convective conditions.
Line Shifts in Rotational Spectra of Polyatomic Chiral Molecules Caused by the Parity Violating Electroweak Interaction

NASA Astrophysics Data System (ADS)

Stohner, J.; Quack, M.

2009-06-01

Are findings in high-energy physics of any importance in molecular spectroscopy ? The answer is clearly `yes'. Energies of enantiomers were considered as exactly equal in an achiral environment, e.g. the gas phase. Today, however, it is well known that this is not valid. The violation of mirror-image symmetry (suggested theoretically and confirmed experimentally in 1956/57) was established in the field of nuclear, high-energy, and atomic physics since then, and it is also the cause for a non-zero energy difference between enantiomers. We expect today that the violation of mirror-image symmetry (parity violation) influences chemistry of chiral molecules as well as their spectroscopy. Progress has been made in the quantitative theoretical prediction of possible spectroscopic signatures of molecular parity violation. The experimental confirmation of parity violation in chiral molecules is, however, still open. Theoretical studies are helpful for the planning and important for a detailed analysis of rovibrational and tunneling spectra of chiral molecules. We report results on frequency shifts in rotational, vibrational and tunneling spectra of some selected chiral molecules which are studied in our group. If time permits, we shall also discuss critically some recent claims of experimental observations of molecular parity violation in condensed phase systems. T. D. Lee, C. N. Yang, Phys. Rev., 104, 254 (1956) C. S. Wu, E. Ambler, R. W. Hayward, D. D. Hoppes, R. P. Hudson, Phys. Rev., 105, 1413 (1957) M. Quack, Angew. Chem. Intl. Ed., 28, 571 (1989) Angew. Chem. Intl. Ed., 41, 4618 (2002) M. Quack, J. Stohner, Chimia, 59, 530 (2005) M. Quack, J. Stohner, M. Willeke, Ann Rev. Phys. Chem. 59, 741 (2008) M. Quack, J. Stohner, Phys. Rev. Lett., 84, 3807 (2000) M. Quack, J. Stohner, J. Chem. Phys., 119, 11228 (2003) J. Stohner, Int. J. Mass Spectrometry 233, 385 (2004) M. Gottselig, M. Quack, J. Stohner, M. Willeke, Int. J. Mass Spectrometry 233, 373 (2004) R. Berger, G. Laubender, M. Quack, A. Sieben, J. Stohner, M. Willeke, Angew. Chem. Intl. Ed., 44, 3623 (2005) J. Stohner, M. Quack, to be published
The Use of ICP-MS and IC-ICP-MS in Environmental and Exposure Assesssment

EPA Science Inventory

OVERVIEW: Application of collision/reaction cell interference reduction technology for the minimization of polyatomic interferences in environmental matrices. Improved risk assessments through the use of arsenic speciation approaches that estimate the bio-accessibility asso...
Rotating full- and reduced-dimensional quantum chemical models of molecules

NASA Astrophysics Data System (ADS)

Fábri, Csaba; Mátyus, Edit; Császár, Attila G.

2011-02-01

A flexible protocol, applicable to semirigid as well as floppy polyatomic systems, is developed for the variational solution of the rotational-vibrational Schrödinger equation. The kinetic energy operator is expressed in terms of curvilinear coordinates, describing the internal motion, and rotational coordinates, characterizing the orientation of the frame fixed to the nonrigid body. Although the analytic form of the kinetic energy operator might be very complex, it does not need to be known a priori within this scheme as it is constructed automatically and numerically whenever needed. The internal coordinates can be chosen to best represent the system of interest and the body-fixed frame is not restricted to an embedding defined with respect to a single reference geometry. The features of the technique mentioned make it especially well suited to treat large-amplitude nuclear motions. Reduced-dimensional rovibrational models can be defined straightforwardly by introducing constraints on the generalized coordinates. In order to demonstrate the flexibility of the protocol and the associated computer code, the inversion-tunneling of the ammonia (14NH3) molecule is studied using one, two, three, four, and six active vibrational degrees of freedom, within both vibrational and rovibrational variational computations. For example, the one-dimensional inversion-tunneling model of ammonia is considered also for nonzero rotational angular momenta. It turns out to be difficult to significantly improve upon this simple model. Rotational-vibrational energy levels are presented for rotational angular momentum quantum numbers J = 0, 1, 2, 3, and 4.
Photoelectron wave function in photoionization: Plane wave or Coulomb wave? [Does photoionization of neutral targets produce Coulomb or plane waves?

DOE PAGES

Gozem, Samer; Gunina, Anastasia O.; Ichino, Takatoshi; ...

2015-10-28

The calculation of absolute total cross sections requires accurate wave functions of the photoelectron and of the initial and final states of the system. The essential information contained in the latter two can be condensed into a Dyson orbital. We employ correlated Dyson orbitals and test approximate treatments of the photoelectron wave function, that is, plane and Coulomb waves, by comparing computed and experimental photoionization and photodetachment spectra. We find that in anions, a plane wave treatment of the photoelectron provides a good description of photodetachment spectra. For photoionization of neutral atoms or molecules with one heavy atom, the photoelectronmore » wave function must be treated as a Coulomb wave to account for the interaction of the photoelectron with the +1 charge of the ionized core. For larger molecules, the best agreement with experiment is often achieved by using a Coulomb wave with a partial (effective) charge smaller than unity. This likely derives from the fact that the effective charge at the centroid of the Dyson orbital, which serves as the origin of the spherical wave expansion, is smaller than the total charge of a polyatomic cation. Finally, the results suggest that accurate molecular photoionization cross sections can be computed with a modified central potential model that accounts for the nonspherical charge distribution of the core by adjusting the charge in the center of the expansion.« less
Molecular Abundances in the Disk of AN Active Galactic Nucleus

NASA Astrophysics Data System (ADS)

Harada, N.; Thompson, T. A.; Herbst, E.

2011-06-01

There are galactic nuclei that emit high luminosities L˜1044-46 erg S-1 including luminosity produced by X-rays from high mass accretion onto the central black holes. These nuclei are called active galactic nuclei (AGNs), and they are accompanied by molecular disks. Observations show high abundances of CN and HCN in the disks; the molecules are proposed to be probes of X-ray dominated regions (XDRs) created by the X-rays from AGNs. We have constructed a spatially-dependent chemical-abundance model of the molecular disk in NGC 1068, a typical AGN-dominated galaxy. Recently, new observations of CN and HCN have been made at much higher spatial resolution, and there are also detections of polyatomic molecules such as HC3N, c-C3H2, and C2H. We discuss how these observations and our simulations can help us to better understand the physical conditions, the disk structure, and conditions for star formation within molecular disks, which are still uncertain. We also include a comparison with other types of galaxies such as (ultra-) luminous infrared galaxies. Usero et al.Astronomy and Astrophysics. 419 (897), 2004. Initial results were presented at the International Symposium on Molecular Spectroscopy 2010, RF05 Garcia-Burillo et al. Astronomy and Astrophysics. 519 (2), 2010. Garcia-Burillo et al. Journal of Physics Conference Series, 131 (12031), 2008. Costagliola et al. ArXiv e-print arXiv:1101.2122, 2011. Nakajima et al. Astrophysical Journal Letters 728 (L38), 2008.
Following the Interstellar History of Carbon: From the Interiors of Stars to the Surfaces of Planets.

PubMed

Ziurys, L M; Halfen, D T; Geppert, W; Aikawa, Y

2016-12-01

The chemical history of carbon is traced from its origin in stellar nucleosynthesis to its delivery to planet surfaces. The molecular carriers of this element are examined at each stage in the cycling of interstellar organic material and their eventual incorporation into solar system bodies. The connection between the various interstellar carbon reservoirs is also examined. Carbon has two stellar sources: supernova explosions and mass loss from evolved stars. In the latter case, the carbon is dredged up from the interior and then ejected into a circumstellar envelope, where a rich and unusual C-based chemistry occurs. This molecular material is eventually released into the general interstellar medium through planetary nebulae. It is first incorporated into diffuse clouds, where carbon is found in polyatomic molecules such as H 2 CO, HCN, HNC, c-C 3 H 2 , and even C 60 + . These objects then collapse into dense clouds, the sites of star and planet formation. Such clouds foster an active organic chemistry, producing compounds with a wide range of functional groups with both gas-phase and surface mechanisms. As stars and planets form, the chemical composition is altered by increasing stellar radiation, as well as possibly by reactions in the presolar nebula. Some molecular, carbon-rich material remains pristine, however, encapsulated in comets, meteorites, and interplanetary dust particles, and is delivered to planet surfaces. Key Words: Carbon isotopes-Prebiotic evolution-Interstellar molecules-Comets-Meteorites. Astrobiology 16, 997-1012.

Phase properties of elastic waves in systems constituted of adsorbed diatomic molecules on the (001) surface of a simple cubic crystal

NASA Astrophysics Data System (ADS)

Deymier, P. A.; Runge, K.

2018-03-01

A Green's function-based numerical method is developed to calculate the phase of scattered elastic waves in a harmonic model of diatomic molecules adsorbed on the (001) surface of a simple cubic crystal. The phase properties of scattered waves depend on the configuration of the molecules. The configurations of adsorbed molecules on the crystal surface such as parallel chain-like arrays coupled via kinks are used to demonstrate not only linear but also non-linear dependency of the phase on the number of kinks along the chains. Non-linear behavior arises for scattered waves with frequencies in the vicinity of a diatomic molecule resonance. In the non-linear regime, the variation in phase with the number of kinks is formulated mathematically as unitary matrix operations leading to an analogy between phase-based elastic unitary operations and quantum gates. The advantage of elastic based unitary operations is that they are easily realizable physically and measurable.
An Algebraic Method for Exploring Quantum Monodromy and Quantum Phase Transitions in Non-Rigid Molecules

NASA Astrophysics Data System (ADS)

Larese, D.; Iachello, F.

2011-06-01

A simple algebraic Hamiltonian has been used to explore the vibrational and rotational spectra of the skeletal bending modes of HCNO, BrCNO, NCNCS, and other ``floppy`` (quasi-linear or quasi-bent) molecules. These molecules have large-amplitude, low-energy bending modes and champagne-bottle potential surfaces, making them good candidates for observing quantum phase transitions (QPT). We describe the geometric phase transitions from bent to linear in these and other non-rigid molecules, quantitatively analysing the spectroscopy signatures of ground state QPT, excited state QPT, and quantum monodromy.The algebraic framework is ideal for this work because of its small calculational effort yet robust results. Although these methods have historically found success with tri- and four-atomic molecules, we now address five-atomic and simple branched molecules such as CH_3NCO and GeH_3NCO. Extraction of potential functions is completed for several molecules, resulting in predictions of barriers to linearity and equilibrium bond angles.
Structure and thermodynamics of asymmetric molecules: Application to linear triatomic dipolar molecules

NASA Astrophysics Data System (ADS)

Nichols, Albert L., III; Calef, Daniel F.

A new method to solve the reference HNC equations is developed to treat systems with both asymmetric short-range and long-range interactions. This method is motivated by the work of Patey and co-workers and uses Lado's free-energy minimizing optimization criteria for the reference HNC approximation. The properties of several fluids composed of linear triatomic molecules with various dipole moments or hard-sphere molecules with different-length dipoles are investigated.
Nonadiabatic effects in ultracold molecules via anomalous linear and quadratic Zeeman shifts.

PubMed

McGuyer, B H; Osborn, C B; McDonald, M; Reinaudi, G; Skomorowski, W; Moszynski, R; Zelevinsky, T

2013-12-13

Anomalously large linear and quadratic Zeeman shifts are measured for weakly bound ultracold 88Sr2 molecules near the intercombination-line asymptote. Nonadiabatic Coriolis coupling and the nature of long-range molecular potentials explain how this effect arises and scales roughly cubically with the size of the molecule. The linear shifts yield nonadiabatic mixing angles of the molecular states. The quadratic shifts are sensitive to nearby opposite f-parity states and exhibit fourth-order corrections, providing a stringent test of a state-of-the-art ab initio model.
Conserved linear dynamics of single-molecule Brownian motion.

PubMed

Serag, Maged F; Habuchi, Satoshi

2017-06-06

Macromolecular diffusion in homogeneous fluid at length scales greater than the size of the molecule is regarded as a random process. The mean-squared displacement (MSD) of molecules in this regime increases linearly with time. Here we show that non-random motion of DNA molecules in this regime that is undetectable by the MSD analysis can be quantified by characterizing the molecular motion relative to a latticed frame of reference. Our lattice occupancy analysis reveals unexpected sub-modes of motion of DNA that deviate from expected random motion in the linear, diffusive regime. We demonstrate that a subtle interplay between these sub-modes causes the overall diffusive motion of DNA to appear to conform to the linear regime. Our results show that apparently random motion of macromolecules could be governed by non-random dynamics that are detectable only by their relative motion. Our analytical approach should advance broad understanding of diffusion processes of fundamental relevance.
Conserved linear dynamics of single-molecule Brownian motion

PubMed Central

Serag, Maged F.; Habuchi, Satoshi

2017-01-01

Macromolecular diffusion in homogeneous fluid at length scales greater than the size of the molecule is regarded as a random process. The mean-squared displacement (MSD) of molecules in this regime increases linearly with time. Here we show that non-random motion of DNA molecules in this regime that is undetectable by the MSD analysis can be quantified by characterizing the molecular motion relative to a latticed frame of reference. Our lattice occupancy analysis reveals unexpected sub-modes of motion of DNA that deviate from expected random motion in the linear, diffusive regime. We demonstrate that a subtle interplay between these sub-modes causes the overall diffusive motion of DNA to appear to conform to the linear regime. Our results show that apparently random motion of macromolecules could be governed by non-random dynamics that are detectable only by their relative motion. Our analytical approach should advance broad understanding of diffusion processes of fundamental relevance. PMID:28585925
Conserved linear dynamics of single-molecule Brownian motion

NASA Astrophysics Data System (ADS)

Serag, Maged F.; Habuchi, Satoshi

2017-06-01

Macromolecular diffusion in homogeneous fluid at length scales greater than the size of the molecule is regarded as a random process. The mean-squared displacement (MSD) of molecules in this regime increases linearly with time. Here we show that non-random motion of DNA molecules in this regime that is undetectable by the MSD analysis can be quantified by characterizing the molecular motion relative to a latticed frame of reference. Our lattice occupancy analysis reveals unexpected sub-modes of motion of DNA that deviate from expected random motion in the linear, diffusive regime. We demonstrate that a subtle interplay between these sub-modes causes the overall diffusive motion of DNA to appear to conform to the linear regime. Our results show that apparently random motion of macromolecules could be governed by non-random dynamics that are detectable only by their relative motion. Our analytical approach should advance broad understanding of diffusion processes of fundamental relevance.
The Spectroscopy and Photophysics of Aniline, 2-AMINOPYRIDINE, and 3-AMINOPYRIDINE

NASA Astrophysics Data System (ADS)

Kim, Byungjoo

1995-01-01

Two-photon ionization photoelectron spectroscopic techniques have been employed in concert with a picosecond laser system and molecular beam machine to study the vibrational structure of molecular ions and the intramolecular dynamics of optically prepared intermediate states. From photoelectron spectra of 2-aminopyridine via various S_1 vibronic resonances, the frequencies of several vibrations in the ionic state are assigned. The ionization potential of the molecule is found to be 8.099 +/- 0.003 eV. Using two-color ionization techniques, the electronic overlap effects in the photoionization of excited molecules have been studied, on the example of 2-aminopyridine, 3-aminopyridine, and aniline. The molecules are excited to their S_1 states, and ionized by a 200 nm laser pulse within 50 ps. The spectra of the aminopyridines show a striking absence of transitions to excited electronic states of the ions, indicating small electronic overlap factors in the ionization transitions and very little configuration interaction in the S _1 states. The spectra of aniline show the vibrationally resolved first excited electronic state band of the ion, which is very weak compared to the ground electronic state band, indicating a small amount of orbital mixing in the S_1 state. The vibrational peaks in the band were assigned by comparison of the spectra via two different vibronic resonances. The observations demonstrate that electronic overlap effects play a very general role in the ionization of polyatomic molecules in electronically excited states, and that orbital mixing patterns of the excited electronic states may become observable by projecting molecular electronic wavefunctions onto the ion states. In the time-delayed experiments for these molecules, all spectra reveal only one product of the nonradiative relaxation process. Careful considerations of electronic and vibrational overlap propensity rules for the ionization step lead to the conclusion that the dominant nonradiative decay mechanism in these molecules is the intersystem crossing to excited vibrational states of the T_1 state. This technique has been applied to study the predissociation process of CS_2 in the S_3 vibronic levels near 200 nm. The spectra show extensive vibrational structure, with unusual activity in the antisymmetric vibrations, indicating the possibility of level mixing in the intermediate state by the IVR couplings.
Analysis of seven salad rocket (Eruca sativa) accessions: The relationships between sensory attributes and volatile and non-volatile compounds.

PubMed

Bell, Luke; Methven, Lisa; Signore, Angelo; Oruna-Concha, Maria Jose; Wagstaff, Carol

2017-03-01

Sensory and chemical analyses were performed on accessions of rocket (Eruca sativa) to determine phytochemical influences on sensory attributes. A trained panel was used to evaluate leaves, and chemical data were obtained for polyatomic ions, amino acids, sugars and organic acids. These chemical data (and data of glucosinolates, flavonols and headspace volatiles previously reported) were used in Principal Component Analysis (PCA) to determine variables statistically important to sensory traits. Significant differences were observed between samples for polyatomic ion and amino acid concentrations. PCA revealed strong, positive correlations between glucosinolates, isothiocyanates and sulfur compounds with bitterness, mustard, peppery, warming and initial heat mouthfeel traits. The ratio between glucosinolates and sugars inferred reduced perception of bitter aftereffects. We highlight the diversity of E. sativa accessions from a sensory and phytochemical standpoint, and the potential for breeders to create varieties that are nutritionally and sensorially superior to existing ones. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.
Linear Arrangement of Motor Protein on a Mechanically Deposited Fluoropolymer Thin Film

NASA Astrophysics Data System (ADS)

Suzuki, Hitoshi; Oiwa, Kazuhiro; Yamada, Akira; Sakakibara, Hitoshi; Nakayama, Haruto; Mashiko, Shinro

1995-07-01

Motor protein molecules such as heavy meromyosin (HMM), one of the major components of skeletal muscle, were arranged linearly on a mechanically deposited fluoropolymer thin film substrate in order to regulate the direction of movement generated by the motor protein. The fluoropolymer film consisted of many linear parallel ridges whose heights and widths were 10 to 20 nm and 10 to 100 nm, respectively. The fluoropolymer ridges adsorbed HMM molecules that were applied onto the film. Actin filaments labeled with rhodamine-phalloidin were observed under a fluorescence microscope moving linearly on the HMM-coated ridges. The observation indicates that HMM molecules were aligned on the fluoropolymer ridges while retaining their function. The velocity of actin movement was measured in this system.
Pseudo-conformer models for linear molecules: Joint treatment of spectroscopic, electron diffraction and ab initio data for the C3O2 molecule

NASA Astrophysics Data System (ADS)

Tarasov, Yury I.; Kochikov, Igor V.

2018-06-01

Dynamic analysis of the molecules with large-amplitude motions (LAM) based on the pseudo-conformer approach has been successfully applied to various molecules. Floppy linear molecules present a special class of molecular structures that possess a pair of conjugate LAM coordinates but allow one-dimensional treatment. In this paper, previously developed treatment for the semirigid molecules is applied to the carbon suboxide molecule. This molecule characterized by the extremely large CCC bending has been thoroughly investigated by spectroscopic and ab initio methods. However, the earlier electron diffraction investigations were performed within a static approach, obtaining thermally averaged parameters. In this paper we apply a procedure aimed at obtaining the short list of self-consistent reference geometry parameters of a molecule, while all thermally averaged parameters are calculated based on reference geometry, relaxation dependencies and quadratic and cubic force constants. We show that such a model satisfactorily describes available electron diffraction evidence with various QC bending potential energy functions when r.m.s. CCC angle is in the interval 151 ± 2°. This leads to a self-consistent molecular model satisfying spectroscopic and GED data. The parameters for linear reference geometry have been defined as re(CO) = 1.161(2) Å and re(CC) = 1.273(2) Å.
Polarization properties of below-threshold harmonics from aligned molecules H2+ in linearly polarized laser fields.

PubMed

Dong, Fulong; Tian, Yiqun; Yu, Shujuan; Wang, Shang; Yang, Shiping; Chen, Yanjun

2015-07-13

We investigate the polarization properties of below-threshold harmonics from aligned molecules in linearly polarized laser fields numerically and analytically. We focus on lower-order harmonics (LOHs). Our simulations show that the ellipticity of below-threshold LOHs depends strongly on the orientation angle and differs significantly for different harmonic orders. Our analysis reveals that this LOH ellipticity is closely associated with resonance effects and the axis symmetry of the molecule. These results shed light on the complex generation mechanism of below-threshold harmonics from aligned molecules.
Vibronic coupling simulations for linear and nonlinear optical processes: Simulation results

NASA Astrophysics Data System (ADS)

Silverstein, Daniel W.; Jensen, Lasse

2012-02-01

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

NASA Astrophysics Data System (ADS)

Clayton, Donald D.; Meyer, Bradley S.

2018-01-01

Our goal is to compute the abundances of carbon atomic complexes that emerge from the C + O cores of core-collapse supernovae. We utilize our chemical reaction network in which every atomic step of growth employs a quantum-mechanically guided reaction rate. This tool follows step-by-step the growth of linear carbon chain molecules from C atoms in the oxygen-rich C + O cores. We postulate that once linear chain molecules reach a sufficiently large size, they isomerize to ringed molecules, which serve as seeds for graphite grain growth. We demonstrate our technique for merging the molecular reaction network with a parallel program that can follow 1017 steps of C addition onto the rare seed species. Due to radioactivity within the C + O core, abundant ambient oxygen is unable to convert C to CO, except to a limited degree that actually facilitates carbon molecular ejecta. But oxygen severely minimizes the linear-carbon-chain abundances. Despite the tiny abundances of these linear-carbon-chain molecules, they can give rise to a small abundance of ringed-carbon molecules that serve as the nucleations on which graphite grain growth builds. We expand the C + O-core gas adiabatically from 6000 K for 109 s when reactions have essentially stopped. These adiabatic tracks emulate the actual expansions of the supernova cores. Using a standard model of 1056 atoms of C + O core ejecta having O/C = 3, we calculate standard ejection yields of graphite grains of all sizes produced, of the CO molecular abundance, of the abundances of linear-carbon molecules, and of Buckminsterfullerene. None of these except CO was expected from the C + O cores just a few years past.
One-dimensional cuts through multidimensional potential-energy surfaces by tunable x rays

NASA Astrophysics Data System (ADS)

Eckert, Sebastian; da Cruz, Vinícius Vaz; Gel'mukhanov, Faris; Ertan, Emelie; Ignatova, Nina; Polyutov, Sergey; Couto, Rafael C.; Fondell, Mattis; Dantz, Marcus; Kennedy, Brian; Schmitt, Thorsten; Pietzsch, Annette; Odelius, Michael; Föhlisch, Alexander

2018-05-01

The concept of the potential-energy surface (PES) and directional reaction coordinates is the backbone of our description of chemical reaction mechanisms. Although the eigenenergies of the nuclear Hamiltonian uniquely link a PES to its spectrum, this information is in general experimentally inaccessible in large polyatomic systems. This is due to (near) degenerate rovibrational levels across the parameter space of all degrees of freedom, which effectively forms a pseudospectrum given by the centers of gravity of groups of close-lying vibrational levels. We show here that resonant inelastic x-ray scattering (RIXS) constitutes an ideal probe for revealing one-dimensional cuts through the ground-state PES of molecular systems, even far away from the equilibrium geometry, where the independent-mode picture is broken. We strictly link the center of gravity of close-lying vibrational peaks in RIXS to a pseudospectrum which is shown to coincide with the eigenvalues of an effective one-dimensional Hamiltonian along the propagation coordinate of the core-excited wave packet. This concept, combined with directional and site selectivity of the core-excited states, allows us to experimentally extract cuts through the ground-state PES along three complementary directions for the showcase H2O molecule.
Interaction Between the Broad-Lined Type Ic Supernova 2012ap and Carriers of Diffuse Interstellar Bands

NASA Technical Reports Server (NTRS)

Milisavljevic, Dan; Margutti, Raffaella; Crabtree, Kyle N.; Foster, Jonathan B.; Soderberg, Alicia M.; Fesen, Robert A.; Parrent, Jerod T.; Sanders, Nathan E.; Drout, Maria R.; Kamble, Atish;

2014-01-01

The diffuse interstellar bands (DIBs) are absorption features observed in optical and near-infrared spectra that are thought to be associated with carbon-rich polyatomic molecules in interstellar gas. However, because the central wavelengths of these bands do not correspond with electronic transitions of any known atomic or molecular species, their nature has remained uncertain since their discovery almost a century ago. Here we report on unusually strong DIBs in optical spectra of the broad- lined Type Ic supernova SN2012ap that exhibit changes in equivalent width over short (. 30 days) timescales. The 4428 A and 6283 A DIB features get weaker with time, whereas the 5780 A feature shows a marginal increase. These nonuniform changes suggest that the supernova is interacting with a nearby source of the DIBs and that the DIB carriers possess high ionization potentials, such as small cations or charged fullerenes. We conclude that moderate-resolution spectra of supernovae with DIB absorptions obtained within weeks of outburst could reveal unique information about the mass-loss environment of their progenitor systems and provide new constraints on the properties of DIB carriers.

Approximate Quantum Dynamics using Ab Initio Classical Separable Potentials: Spectroscopic Applications.

PubMed

Hirshberg, Barak; Sagiv, Lior; Gerber, R Benny

2017-03-14

Algorithms for quantum molecular dynamics simulations that directly use ab initio methods have many potential applications. In this article, the ab initio classical separable potentials (AICSP) method is proposed as the basis for approximate algorithms of this type. The AICSP method assumes separability of the total time-dependent wave function of the nuclei and employs mean-field potentials that govern the dynamics of each degree of freedom. In the proposed approach, the mean-field potentials are determined by classical ab initio molecular dynamics simulations. The nuclear wave function can thus be propagated in time using the effective potentials generated "on the fly". As a test of the method for realistic systems, calculations of the stationary anharmonic frequencies of hydrogen stretching modes were carried out for several polyatomic systems, including three amino acids and the guanine-cytosine pair of nucleobases. Good agreement with experiments was found. The method scales very favorably with the number of vibrational modes and should be applicable for very large molecules, e.g., peptides. The method should also be applicable for properties such as vibrational line widths and line shapes. Work in these directions is underway.
Ultrasensitive detection of atmospheric trace gases using frequency modulation spectroscopy

NASA Technical Reports Server (NTRS)

Cooper, David E.

1986-01-01

Frequency modulation (FM) spectroscopy is a new technique that promises to significantly extend the state-of-the-art in point detection of atmospheric trace gases. FM spectroscopy is essentially a balanced bridge optical heterodyne approach in which a small optical absorption or dispersion from an atomic or molecular species of interest generates an easily detected radio frequency (RF) signal. This signal can be monitored using standard RF signal processing techniques and is, in principle, limited only by the shot noise generated in the photodetector by the laser source employed. The use of very high modulation frequencies which exceed the spectral width of the probed absorption line distinguishes this technique from the well-known derivative spectroscopy which makes use of low (kHz) modulation frequencies. FM spectroscopy was recently extended to the 10 micron infrared (IR) spectral region where numerous polyatomic molecules exhibit characteristic vibrational-rotational bands. In conjunction with tunable semiconductor diode lasers, the quantum-noise-limited sensitivity of the technique should allow for the detection of absorptions as small as .00000001 in the IR spectral region. This sensitivity would allow for the detection of H2O2 at concentrations as low as 1 pptv with an integration time of 10 seconds.
Native Frames: Disentangling Sequential from Concerted Three-Body Fragmentation

NASA Astrophysics Data System (ADS)

Rajput, Jyoti; Severt, T.; Berry, Ben; Jochim, Bethany; Feizollah, Peyman; Kaderiya, Balram; Zohrabi, M.; Ablikim, U.; Ziaee, Farzaneh; Raju P., Kanaka; Rolles, D.; Rudenko, A.; Carnes, K. D.; Esry, B. D.; Ben-Itzhak, I.

2018-03-01

A key question concerning the three-body fragmentation of polyatomic molecules is the distinction of sequential and concerted mechanisms, i.e., the stepwise or simultaneous cleavage of bonds. Using laser-driven fragmentation of OCS into O++C++S+ and employing coincidence momentum imaging, we demonstrate a novel method that enables the clear separation of sequential and concerted breakup. The separation is accomplished by analyzing the three-body fragmentation in the native frame associated with each step and taking advantage of the rotation of the intermediate molecular fragment, CO2 + or CS2 + , before its unimolecular dissociation. This native-frame method works for any projectile (electrons, ions, or photons), provides details on each step of the sequential breakup, and enables the retrieval of the relevant spectra for sequential and concerted breakup separately. Specifically, this allows the determination of the branching ratio of all these processes in OCS3 + breakup. Moreover, we find that the first step of sequential breakup is tightly aligned along the laser polarization and identify the likely electronic states of the intermediate dication that undergo unimolecular dissociation in the second step. Finally, the separated concerted breakup spectra show clearly that the central carbon atom is preferentially ejected perpendicular to the laser field.
Time-resolved multi-mass ion imaging: Femtosecond UV-VUV pump-probe spectroscopy with the PImMS camera.

PubMed

Forbes, Ruaridh; Makhija, Varun; Veyrinas, Kévin; Stolow, Albert; Lee, Jason W L; Burt, Michael; Brouard, Mark; Vallance, Claire; Wilkinson, Iain; Lausten, Rune; Hockett, Paul

2017-07-07

The Pixel-Imaging Mass Spectrometry (PImMS) camera allows for 3D charged particle imaging measurements, in which the particle time-of-flight is recorded along with (x, y) position. Coupling the PImMS camera to an ultrafast pump-probe velocity-map imaging spectroscopy apparatus therefore provides a route to time-resolved multi-mass ion imaging, with both high count rates and large dynamic range, thus allowing for rapid measurements of complex photofragmentation dynamics. Furthermore, the use of vacuum ultraviolet wavelengths for the probe pulse allows for an enhanced observation window for the study of excited state molecular dynamics in small polyatomic molecules having relatively high ionization potentials. Herein, preliminary time-resolved multi-mass imaging results from C 2 F 3 I photolysis are presented. The experiments utilized femtosecond VUV and UV (160.8 nm and 267 nm) pump and probe laser pulses in order to demonstrate and explore this new time-resolved experimental ion imaging configuration. The data indicate the depth and power of this measurement modality, with a range of photofragments readily observed, and many indications of complex underlying wavepacket dynamics on the excited state(s) prepared.

Sudoku Puzzles as Chemistry Learning Tools

ERIC Educational Resources Information Center

Crute, Thomas D.; Myers, Stephanie A.

2007-01-01

A sudoku puzzle was designed that incorporated lists of chemistry terms like polyatomic ions, organic functional groups or strong nucleophiles that students need to learn. It was found that students enjoyed solving such puzzles and also such puzzles made the boring tasks of memorizing basic chemical terms an exciting one.
Hyperspherical nuclear motion of H3 + and D3 + in the electronic triplet state, a 3Sigmau +.

PubMed

Ferreira, Tiago Mendes; Alijah, Alexander; Varandas, António J C

2008-02-07

The potential energy surface of H(3) (+) in the lowest electronic triplet state, a (3)Sigma(u) (+), shows three equivalent minima at linear nuclear configurations. The vibrational levels of H(3) (+) and D(3) (+) on this surface can therefore be described as superimposed linear molecule states. Owing to such a superposition, each vibrational state characterized by quantum numbers of an isolated linear molecule obtains a one- and a two-dimensional component. The energy splittings between the two components have now been rationalized within a hyperspherical picture. It is shown that nuclear motion along the hyperangle phi mainly accounts for the splittings and provides upper bounds. This hyperspherical motion can be considered an extension of the antisymmetric stretching motion of the individual linear molecule.
Full-dimensional treatment of short-time vibronic dynamics in a molecular high-order-harmonic-generation process in methane

NASA Astrophysics Data System (ADS)

Patchkovskii, Serguei; Schuurman, Michael S.

2017-11-01

We present derivation and implementation of the multiconfigurational strong-field approximation with Gaussian nuclear wave packets (MC-SFA-GWP)—a version of the molecular strong-field approximation which treats all electronic and nuclear degrees of freedom, including their correlations, quantum mechanically. The technique allows realistic simulation of high-order-harmonic emission in polyatomic molecules without invoking reduced-dimensionality models for the nuclear motion or the electronic structure. We use MC-SFA-GWP to model isotope effects in high-order-harmonic-generation (HHG) spectroscopy of methane. The HHG emission in this molecule transiently involves the strongly vibronically coupled F22 electronic state of the CH4+ cation. We show that the isotopic HHG ratio in methane contains signatures of (a) field-free vibronic dynamics at the conical intersection (CI); (b) resonant features in the recombination cross sections; (c) laser-driven bound-state dynamics; as well as (d) the well-known short-time Gaussian decay of the emission. We assign the intrinsic vibronic feature (a) to a relatively long-lived (≥4 fs) vibronic wave packet of the singly excited ν4 (t2) and ν2 (e ) vibrational modes, strongly coupled to the components of the F22 electronic state. We demonstrate that these physical effects differ in their dependence on the wavelength, intensity, and duration of the driving pulse, allowing them to be disentangled. We thus show that HHG spectroscopy provides a versatile tool for exploring both conical intersections and resonant features in photorecombination matrix elements in the regime not easily accessible with other techniques.
Stereodynamics of the reactions: F + H2/HD/HT→FH + H/D/T

NASA Astrophysics Data System (ADS)

Chi, Xiao-Lin; Zhao, Jin-Feng; Zhang, Yong-Jia; Ma, Feng-Cai; Li, Yong-Qing

2015-05-01

Among many kinds of ways to study the properties of atom and molecule collision, the quasi-classical trajectory (QCT) method is an effective one to investigate the molecular reaction dynamics. QCT calculations have been carried out to investigate the stereodynamics of the reactions F + H2/HD/HT→FH + H/D/T, which proceed on the lowest-lying electronic states of the FH2 system based on the potential energy surface (PES) of the 12A’ FH2 ground state. Although the QCT method cannot describe all quantum effects in the process of the reaction, it has unique advantages when facing a three-atoms system or complicated polyatomic systems. Differential cross sections (DCSs) and three angle distribution functions P(θr), P(ϕr), P(θr, ϕr) on the PES at the collision of 2.74 kcal/mol have been investigated. The isotope effect becomes more obvious with the reagent molecule H2 turning into HD and HT. P(θr, ϕr), as the joint probability density function of both polar angles θr and ϕr, can reflect the properties of three-dimensional dynamic more intuitively. Project supported by the National Natural Science Foundation of China (Grant No. 11474141), the Scientific Research Foundation for the Returned Overseas Chinese Scholars (Grant No. 2014-1685), the Scientific Research Foundation for the Doctor of Liaoning University, the Special Fund Based Research New Technology of Methanol Conversion and Coal Instead of Oil, and the China Postdoctoral Science Foundation (Grant No. 2014M550158).
Rotational and vibrotational transfer in H*-CO2 collisions: The influence of stereokinematic restrictions

NASA Astrophysics Data System (ADS)

Clare, Suzanne; Marks, Alison J.; McCaffery, Anthony J.

1999-11-01

We describe a quantitative angular momentum (AM) model for predicting rotational transfer (RT) and vibrotational transfer (VRT) in collisions between CO2 and hot H atoms. This molecule is important in several contexts, not least as a bridge between the relative simplicity of diatomic molecules and the complexities of polyatomic RT and VRT. We show that for pure RT, an AM constraint dominates but that this changes to a dominant energetic constraint in the case of VRT. The requirement that the (001) vibrational channel be opened simultaneously with the generation of AM imposes special restrictions which effectively limit the trajectories that lead to VRT. The origin of this is a constraint-induced restriction on the effective impact parameter (bnmax) for individual Δj channels and the effect is manifest as reduced probability for populating low Δj channels. In CO2-H* this leads to a shift in the peak of (VRT) Δj probabilities away from zero as found experimentally for the (001) vibrational mode. We report a Monte Carlo trajectory calculation similar to that of Kreutz and Flynn [J. Chem. Phys. 93, 452 (1990)] but predict an exponential-like dependence of pure RT on Δj. For VRT to (001) the constraint-induced restrictions on bnmax are incorporated quantitatively and the vibrational channel-opening velocity is treated as a vector quantity. The results of these calculations are in good agreement with experiment. The underlying mechanism, likely to be general in VRT, is clearly revealed in plots of relative velocity versus rotational AM change.
Highly Resolved Studies of Vacuum Ultraviolet Photoionization Dynamics

NASA Astrophysics Data System (ADS)

Kakar, Sandeep

We use measurements of dispersed fluorescence from electronically excited photoions to study fundamental aspects of intramolecular dynamics. Our experimental innovations make it possible to obtain highly resolved photoionization data that offer qualitative insights into molecular scattering. In particular, we obtain vibrationally resolved data to probe coupling between the electronic and nuclear degrees of freedom by studying the distribution of vibrational energy among photoions. Vibrationally resolved branching ratios are measured over a broad spectral range of excitation energy and their non-Franck-Condon behavior is used as a tool to investigate two diverse aspects of shape resonant photoionization. First, vibrational branching ratios are obtained for the SiF_4 5a _1^{-1} and CS_2 5sigma_{rm u} ^{-1} photoionization channels to help elucidate the microscopic aspects of shape resonant wavefunction for polyatomic molecules. It is shown that in such molecules the shape resonant wavefunction is not necessarily attributable to a specific bond in the molecule. Second, the multichannel aspect of shape resonant photoionization dynamics, reflected in continuum channel coupling, is investigated by obtaining vibrational branching ratios for the 2 sigma_{rm u}^{ -1} and 4sigma^{ -1} photoionization of the isoelectronic molecules N_2 and CO, respectively. These data indicate that effects of continuum coupling may be widespread. We also present the first set of rotationally resolved data over a wide energy range for the 2 sigma_{rm u}^{ -1} photoionization of N_2. These data probe the partitioning of the angular momentum between the photoelectron and photoion, and highlight the multicenter nature of the molecular potential. These case studies illustrate the utility of dispersed fluorescence measurements as a complement to photoelectron spectroscopy for obtaining highly resolved data for molecular photoionization. These measurements makes it possible to probe intrinsically molecular aspects, such as the vibration and rotation, of photoionization dynamics over an extended spectral range when used in conjunction with synchrotron radiation as the exciting source. Furthermore, the high resolution made possible by this technique provides high selectivity for accessing weaker ionization channels which are the ones strongly affected by resonant activity, and the present study repeatedly stresses the importance of this capability in discovering and deciphering new trends in resonant molecular ionization dynamics.
Ab initio multiple spawning dynamics study of dimethylnitramine and dimethylnitramine-Fe complex to model their ultrafast nonadiabatic chemistry

NASA Astrophysics Data System (ADS)

Bera, Anupam; Ghosh, Jayanta; Bhattacharya, Atanu

2017-07-01

Conical intersections are now firmly established to be the key features in the excited electronic state processes of polyatomic energetic molecules. In the present work, we have explored conical intersection-mediated nonadiabatic chemical dynamics of a simple analogue nitramine molecule, dimethylnitramine (DMNA, containing one N-NO2 energetic group), and its complex with an iron atom (DMNA-Fe). For this task, we have used the ab initio multiple spawning (AIMS) dynamics simulation at the state averaged-complete active space self-consistent field(8,5)/6-31G(d) level of theory. We have found that DMNA relaxes back to the ground (S0) state following electronic excitation to the S1 excited state [which is an (n,π*) excited state] with a time constant of approximately 40 fs. This AIMS result is in very good agreement with the previous surface hopping-result and femtosecond laser spectroscopy result. DMNA does not dissociate during this fast internal conversion from the S1 to the S0 state. DMNA-Fe also undergoes extremely fast relaxation from the upper S1 state to the S0 state; however, this relaxation pathway is dissociative in nature. DMNA-Fe undergoes initial Fe-O, N-O, and N-N bond dissociations during relaxation from the upper S1 state to the ground S0 state through the respective conical intersection. The AIMS simulation reveals the branching ratio of these three channels as N-N:Fe-O:N-O = 6:3:1 (based on 100 independent simulations). Furthermore, the AIMS simulation reveals that the Fe-O bond dissociation channel exhibits the fastest (time constant 24 fs) relaxation, while the N-N bond dissociation pathway features the slowest (time constant 128 fs) relaxation. An intermediate time constant (30 fs) is found for the N-O bond dissociation channel. This is the first nonadiabatic chemical dynamics study of metal-contained energetic molecules through conical intersections.
Investigation of the ellipsoidal-statistical Bhatnagar-Gross-Krook kinetic model applied to gas-phase transport of heat and tangential momentum between parallel walls

NASA Astrophysics Data System (ADS)

Gallis, M. A.; Torczynski, J. R.

2011-03-01

The ellipsoidal-statistical Bhatnagar-Gross-Krook (ES-BGK) kinetic model is investigated for steady gas-phase transport of heat, tangential momentum, and mass between parallel walls (i.e., Fourier, Couette, and Fickian flows). This investigation extends the original study of Cercignani and Tironi, who first applied the ES-BGK model to heat transport (i.e., Fourier flow) shortly after this model was proposed by Holway. The ES-BGK model is implemented in a molecular-gas-dynamics code so that results from this model can be compared directly to results from the full Boltzmann collision term, as computed by the same code with the direct simulation Monte Carlo (DSMC) algorithm of Bird. A gas of monatomic molecules is considered. These molecules collide in a pairwise fashion according to either the Maxwell or the hard-sphere interaction and reflect from the walls according to the Cercignani-Lampis-Lord model with unity accommodation coefficients. Simulations are performed at pressures from near-free-molecular to near-continuum. Unlike the BGK model, the ES-BGK model produces heat-flux and shear-stress values that both agree closely with the DSMC values at all pressures. However, for both interactions, the ES-BGK model produces molecular-velocity-distribution functions that are qualitatively similar to those determined for the Maxwell interaction from Chapman-Enskog theory for small wall temperature differences and moment-hierarchy theory for large wall temperature differences. Moreover, the ES-BGK model does not produce accurate values of the mass self-diffusion coefficient for either interaction. Nevertheless, given its reasonable accuracy for heat and tangential-momentum transport, its sound theoretical foundation (it obeys the H-theorem), and its available extension to polyatomic molecules, the ES-BGK model may be a useful method for simulating certain classes of single-species noncontinuum gas flows, as Cercignani suggested.
Science at the Time-scale of the Electron

NASA Astrophysics Data System (ADS)

Murnane, Margaret

2010-03-01

Replace this text with your abstract Ever since the invention of the laser 50 years ago and its application in nonlinear optics, scientists have been striving to extend coherent laser beams into the x-ray region of the spectrum. Very recently however, the prospects for tabletop coherent sources, with attosecond pulse durations, at very short wavelengths even in the hard x-ray region of the spectrum at wavelengths < 1nm, have brightened considerably. These advances are possible by taking nonlinear optics techniques to an extreme, and are the direct result of a new ability to manipulate electrons on the fastest, attosecond, time-scales of our natural world. My talk will discuss new experimental data that demonstrates high harmonic generation of laser-like, fully coherent, 10 attosecond duration, soft x-ray beams at photon energies around 0.5keV. Several applications will also be discussed, including making a movie of how electron orbitals in a molecule change shape as a molecule breaks apart, following how fast a magnetic material can flip orientation, understanding how fast heat flows in a nanocircuit, or building a microscope without lenses. [4pt] [1] T. Popmintchev et al., ``Phase matched upconversion of coherent ultrafast laser light into the soft and hard x-ray regions of the spectrum'', PNAS 106, 10516 (2009). [0pt] [2] C. LaOVorakiat et al., ``Ultrafast Soft X-Ray Magneto-Optics at the M-edge Using a Tabletop High-Harmonic Source'', Physical Review Letters 103, 257402 (2009). [0pt] [3] M. Siemens et al. ``Measurement of quasi-ballistic heat transport across nanoscale interfaces using ultrafast coherent soft x-ray beams'', Nature Materials 9, 26 (2010). [0pt] [4] K. Raines et al., ``Three-dimensional structure determination from a single view,'' Nature 463, 214 (2010). [0pt] [5] W. Li et al., ``Time-resolved Probing of Dynamics in Polyatomic Molecules using High Harmonic Generation'', Science 322, 1207 (2008).
An implicit boundary integral method for computing electric potential of macromolecules in solvent

NASA Astrophysics Data System (ADS)

Zhong, Yimin; Ren, Kui; Tsai, Richard

2018-04-01

A numerical method using implicit surface representations is proposed to solve the linearized Poisson-Boltzmann equation that arises in mathematical models for the electrostatics of molecules in solvent. The proposed method uses an implicit boundary integral formulation to derive a linear system defined on Cartesian nodes in a narrowband surrounding the closed surface that separates the molecule and the solvent. The needed implicit surface is constructed from the given atomic description of the molecules, by a sequence of standard level set algorithms. A fast multipole method is applied to accelerate the solution of the linear system. A few numerical studies involving some standard test cases are presented and compared to other existing results.
The effect of aged litter materials on polyatomic ion concentrations in fractionated suspended particulate matter from broiler house

USDA-ARS?s Scientific Manuscript database

Inorganic emissions from livestock production and subsequent deposition of these ions can be a major source of pollution, causing nitrogen enrichment, eutrophication, acidification of soils and surface waters, and aerosol formation. In the poultry house, ammonia and hydrogen sulfide emissions can a...
Ion dehydration controls adsorption at the micellar interface: hydrotropic ions.

PubMed

Lima, Filipe S; Andrade, Marcos F C; Mortara, Laura; Gustavo Dias, Luís; Cuccovia, Iolanda M; Chaimovich, Hernan

2017-11-22

The properties of ionic micelles depend on the nature of the counterion, and these effects become more evident as the ion adsorption at the interface increases. Prediction of the relative extent of ion adsorption is required for rational design of ionic micellar aggregates. Unlike the well understood adsorption of monatomic ions, the adsorption of polyatomic ions is not easily predicted. We combined experimental and computational methods to evaluate the affinity of hydrotropic ions, i.e., ions with polar and apolar regions, to the surface of positively charged micelles. We analyzed cationic micelles of dodecyltrimethylammonium and six hydrotropic counterions: methanesulfonate, trifluoromethanesulfonate, benzenesulfonate, acetate, trifluoroacetate and benzoate. Our results demonstrated that the apolar region of hydrotropic ions had the largest influence on micellar properties. The dehydration of the apolar region of hydrotropic ions upon their adsorption at the micellar interface determined the ion adsorption extension, differently to what was expected based on Collins' law of matching affinities. These results may lead to more general models to describe the adsorption of ions, including polyatomic ions, at the micellar interface.
Developing Density of Laser-Cooled Neutral Atoms and Molecules in a Linear Magnetic Trap

NASA Astrophysics Data System (ADS)

Velasquez, Joe, III; Walstrom, Peter; di Rosa, Michael

2013-05-01

In this poster we show that neutral particle injection and accumulation using laser-induced spin flips may be used to form dense ensembles of ultracold magnetic particles, i.e., laser-cooled paramagnetic atoms and molecules. Particles are injected in a field-seeking state, are switched by optical pumping to a field-repelled state, and are stored in the minimum-B trap. The analogous process in high-energy charged-particle accumulator rings is charge-exchange injection using stripper foils. The trap is a linear array of sextupoles capped by solenoids. Particle-tracking calculations and design of our linear accumulator along with related experiments involving 7Li will be presented. We test these concepts first with atoms in preparation for later work with selected molecules. Finally, we present our preliminary results with CaH, our candidate molecule for laser cooling. This project is funded by the LDRD program of Los Alamos National Laboratory.
Determination of low concentrations of iron, arsenic, selenium, cadmium, and other trace elements in natural samples using an octopole collision/reaction cell equipped quadrupole-inductively coupled plasma mass spectrometer.

PubMed

Dial, Angela R; Misra, Sambuddha; Landing, William M

2015-04-30

Accurate determination of trace metals has many applications in environmental and life sciences, such as constraining the cycling of essential micronutrients in biological production and employing trace metals as tracers for anthropogenic pollution. Analysis of elements such as Fe, As, Se, and Cd is challenged by the formation of polyatomic mass spectrometric interferences, which are overcome in this study. We utilized an Octopole Collision/Reaction Cell (CRC)-equipped Quadrupole-Inductively Coupled Plasma Mass Spectrometer for the rapid analysis of small volume samples (~250 μL) in a variety of matrices containing HNO3 and/or HCl. Efficient elimination of polyatomic interferences was demonstrated by the use of the CRC in Reaction Mode (RM; H2 gas) and in Collision-Reaction Mode (CRM; H2 and He gas), in addition to hot plasma (RF power 1500 W) and cool plasma (600 W) conditions. It was found that cool plasma conditions with RM achieved the greatest signal sensitivity while maintaining low detection limits (i.e. (56) Fe in 0.44 M HNO3 has a sensitivity of 160,000 counts per second (cps)-per-1 µg L(-1) and a limit of detection (LoD) of 0.86 ng L(-1) ). The average external precision was ≤ ~10% for minor (≤10 µg L(-1) ) elements measured in a 1:100 dilution of NIST 1643e and for iron in rainwater samples under all instrumental operating conditions. An improved method has been demonstrated for the rapid multi-element analysis of trace metals that are challenged by polyatomic mass spectrometric interferences, with a focus on (56) Fe, (75) As, (78) Se and (111) Cd. This method can contribute to aqueous environmental geochemistry and chemical oceanography, as well as other fields such as forensic chemistry, agriculture, food chemistry, and pharmaceutical sciences. Copyright © 2015 John Wiley & Sons, Ltd.
Comparison of the Single Molecule Dynamics of Linear and Circular DNAs in Planar Extensional Flows

NASA Astrophysics Data System (ADS)

Li, Yanfei; Hsiao, Kai-Wen; Brockman, Christopher; Yates, Daniel; McKenna, Gregory; Schroeder, Charles; San Francisco, Michael; Kornfield, Julie; Anderson, Rae

2015-03-01

Chain topology has a profound impact on the flow behaviors of single macromolecules. The absence of free ends separates circular polymers from other chain architectures, i.e., linear, star, and branched. In the present work, we study the single chain dynamics of large circular and linear DNA molecules by comparing the relaxation dynamics, steady state coil-stretch transition, and transient molecular individualism behaviors for the two types of macromolecules. To this end, large circular DNA molecules were biologically synthesized and studied in a microfluidic device that has a cross-slot geometry to develop a stagnation point extensional flow. Although the relaxation time of rings scales in the same way as for the linear analog, the circular polymers show quantitatively different behaviors in the steady state extension and qualitatively different behaviors during a transient stretch. The existence of some commonality between these two topologies is proposed. Texas Tech University John R. Bradford Endowment.
Entropic potential field formed for a linear-motor protein near a filament: Statistical-mechanical analyses using simple models.

PubMed

Amano, Ken-Ichi; Yoshidome, Takashi; Iwaki, Mitsuhiro; Suzuki, Makoto; Kinoshita, Masahiro

2010-07-28

We report a new progress in elucidating the mechanism of the unidirectional movement of a linear-motor protein (e.g., myosin) along a filament (e.g., F-actin). The basic concept emphasized here is that a potential field is entropically formed for the protein on the filament immersed in solvent due to the effect of the translational displacement of solvent molecules. The entropic potential field is strongly dependent on geometric features of the protein and the filament, their overall shapes as well as details of the polyatomic structures. The features and the corresponding field are judiciously adjusted by the binding of adenosine triphosphate (ATP) to the protein, hydrolysis of ATP into adenosine diphosphate (ADP)+Pi, and release of Pi and ADP. As the first step, we propose the following physical picture: The potential field formed along the filament for the protein without the binding of ATP or ADP+Pi to it is largely different from that for the protein with the binding, and the directed movement is realized by repeated switches from one of the fields to the other. To illustrate the picture, we analyze the spatial distribution of the entropic potential between a large solute and a large body using the three-dimensional integral equation theory. The solute is modeled as a large hard sphere. Two model filaments are considered as the body: model 1 is a set of one-dimensionally connected large hard spheres and model 2 is a double helical structure formed by two sets of connected large hard spheres. The solute and the filament are immersed in small hard spheres forming the solvent. The major findings are as follows. The solute is strongly confined within a narrow space in contact with the filament. Within the space there are locations with sharply deep local potential minima along the filament, and the distance between two adjacent locations is equal to the diameter of the large spheres constituting the filament. The potential minima form a ringlike domain in model 1 while they form a pointlike one in model 2. We then examine the effects of geometric features of the solute on the amplitudes and asymmetry of the entropic potential field acting on the solute along the filament. A large aspherical solute with a cleft near the solute-filament interface, which mimics the myosin motor domain, is considered in the examination. Thus, the two fields in our physical picture described above are qualitatively reproduced. The factors to be taken into account in further studies are also discussed.
Linear indices of the "molecular pseudograph's atom adjacency matrix": definition, significance-interpretation, and application to QSAR analysis of flavone derivatives as HIV-1 integrase inhibitors.

PubMed

Marrero-Ponce, Yovani

2004-01-01

This report describes a new set of molecular descriptors of relevance to QSAR/QSPR studies and drug design, atom linear indices fk(xi). These atomic level chemical descriptors are based on the calculation of linear maps on Rn[fk(xi): Rn--> Rn] in canonical basis. In this context, the kth power of the molecular pseudograph's atom adjacency matrix [Mk(G)] denotes the matrix of fk(xi) with respect to the canonical basis. In addition, a local-fragment (atom-type) formalism was developed. The kth atom-type linear indices are calculated by summing the kth atom linear indices of all atoms of the same atom type in the molecules. Moreover, total (whole-molecule) linear indices are also proposed. This descriptor is a linear functional (linear form) on Rn. That is, the kth total linear indices is a linear map from Rn to the scalar R[ fk(x): Rn --> R]. Thus, the kth total linear indices are calculated by summing the atom linear indices of all atoms in the molecule. The features of the kth total and local linear indices are illustrated by examples of various types of molecular structures, including chain-lengthening, branching, heteroatoms-content, and multiple bonds. Additionally, the linear independence of the local linear indices to other 0D, 1D, 2D, and 3D molecular descriptors is demonstrated by using principal component analysis for 42 very heterogeneous molecules. Much redundancy and overlapping was found among total linear indices and most of the other structural indices presently in use in the QSPR/QSAR practice. On the contrary, the information carried by atom-type linear indices was strikingly different from that codified in most of the 229 0D-3D molecular descriptors used in this study. It is concluded that the local linear indices are an independent indices containing important structural information to be used in QSPR/QSAR and drug design studies. In this sense, atom, atom-type, and total linear indices were used for the prediction of pIC50 values for the cleavage process of a set of flavone derivatives inhibitors of HIV-1 integrase. Quantitative models found are significant from a statistical point of view (R of 0.965, 0.902, and 0.927, respectively) and permit a clear interpretation of the studied properties in terms of the structural features of molecules. A LOO cross-validation procedure revealed that the regression models had a fairly good predictability (q2 of 0.679, 0.543, and 0.721, respectively). The comparison with other approaches reveals good behavior of the method proposed. The approach described in this paper appears to be an excellent alternative or guides for discovery and optimization of new lead compounds.
Study of Polyatomic Dynamics in the Atmosphere.

DTIC Science & Technology

1987-03-25

phere and the Shuttle ram glow. Ihij~pijj erif of th0 . repiir I ds’-vr ihes work carriled nio in the IAIfli V The~ prodi’ j "v of~ t~t electron beam...8217 diatomics-in -mole- Symposium on Molecular Spectroscopy, Ohio State University, Colum- bus , Ohio, June 1935.cules PES for Hj* is used the fundamental
Control of π-Electron Rotations in Chiral Aromatic Molecules Using Intense Laser Pulses

NASA Astrophysics Data System (ADS)

Kanno, Manabu; Kono, Hirohiko; Fujimura, Yuichi

Our recent theoretical studies on laser-induced π-electron rotations in chiral aromatic molecules are reviewed. π electrons of a chiral aromatic molecule can be rotated along its aromatic ring by a nonhelical, linearly polarized laser pulse. An ansa aromatic molecule with a six-membered ring, 2,5-dichloro[n](3,6) pyrazinophane, which belongs to a planar-chiral molecule group, and its simplified molecule 2,5-dichloropyrazine are taken as model molecules. Electron wavepacket simulations in the frozen-molecular-vibration approximation show that the initial direction of π-electron rotation depends on the polarization direction of a linearly polarized laser pulse applied. Consecutive unidirectional rotation can be achieved by applying a sequence of linearly polarized pump and dump pulses to prevent reverse rotation. Optimal control simulations of π-electron rotation show that another controlling factor for unidirectional rotation is the relative optical phase between the different frequency components of an incident pulse in addition to photon polarization direction. Effects of nonadiabatic coupling between π-electron rotation and molecular vibrations are also presented, where the constraints of the frozen approximation are removed. The angular momentum gradually decays mainly owing to nonadiabatic coupling, while the vibrational amplitudes greatly depend on their rotation direction. This suggests that the direction of π-electron rotation on an attosecond timescale can be identified by detecting femtosecond molecular vibrations.
Translation and integration of numerical atomic orbitals in linear molecules

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

Heinäsmäki, Sami, E-mail: sami.heinasmaki@gmail.com

2014-02-14

We present algorithms for translation and integration of atomic orbitals for LCAO calculations in linear molecules. The method applies to arbitrary radial functions given on a numerical mesh. The algorithms are based on pseudospectral differentiation matrices in two dimensions and the corresponding two-dimensional Gaussian quadratures. As a result, multicenter overlap and Coulomb integrals can be evaluated effectively.

Detection of ultratrace phosphorus and sulfur by quadrupole ICPMS with dynamic reaction cell.

PubMed

Bandura, Dmitry R; Baranov, Vladimir I; Tanner, Scott D

2002-04-01

A method of detection of ultratrace phosphorus and sulfur that uses reaction with O2 in a dynamic reaction cell (DRC) to oxidize S+ and P+ to allow their detection as SO+ and PO+ is described. The method reduces the effect of polyatomic isobaric interferences at m/z = 31 and 32 by detecting P+ and S+ as the product oxide ions that are less interfered. Use of an axial field in the DRC improves transmission of the product oxide ions 4-6 times. With no axial field, detection limits (3sigma, 5-s integration) of 0.20 and 0.52 ng/mL, with background equivalent concentrations of 0.53 and 4.8 ng/mL, respectively, are achieved. At an optimum axial field potential (200 V), the detection limits are 0.06 ng/mL for P and 0.2 ng/mL for S, respectively. The method is used for determining the degree of phosphorylation of beta-casein, and regular and dephosphorylated alpha-caseins at 10-1000 fmol/microL concentration, with 5-10% v/v organic sample matrix (acetonitrile, formic acid, ammonium bicarbonate). The measured degree of phosphorylation for beta-casein (4.9 phosphorus atoms/molecule) and regular alpha-casein (8.8 phoshorus atoms/molecule) are in good agreement with the structural data for the proteins. The P/S ratio for regular alpha-casein (1.58) is in good agreement with the ratio of the number of phosphorylation sites to the number of sulfur-containing amino acid residues cysteine and methionine. The P/S ratio for commercially available dephosphorylated alpha-casein is measured at 0.41 (approximately 26% residual phosphate).
Diatomics-in-molecules description of the Rg-Hal2 rare gas-halogen van der Waals complexes with applications to He-Cl2

NASA Astrophysics Data System (ADS)

Grigorenko, B. L.; Nemukhin, A. V.; Buchachenko, A. A.; Stepanov, N. F.; Umanskii, S. Ya.

1997-03-01

The diatomics-in-molecules (DIM) technique is applied for a description of the low-lying states of the Rg-Hal2 van der Waals complexes correlating with the lowest states of constituent atoms Rg(1S)+Hal(2Pj)+Hal(2Pj). The important feature of this approach is the construction of polyatomic basis functions as products of the Hal2 diatomic eigenstates classified within the Hund "c" scheme and the atomic rare gas wave function. Necessary transformations to the other basis set representations are described, and finally all the matrix elements are expressed in terms of nonrelativistic adiabatic energies of Hal2 and Rg Hal fragments and spin-orbit splitting constant of the halogen atom. Our main concern is to test the DIM-based approximations of different levels taking the He-Cl2 system as an example. Namely, we have compared the results obtained within a hierarchy of approaches: (1) the simplest pairwise potential scheme as a far extreme of the DIM model, (2) the same as (1) but with the different components (Σ and Π) for He-Cl interaction, (3) the accurate DIM technique without spin-orbit terms, and (4) the highest level which takes into account all these contributions. The results have been compared to the other DIM like models as well. The shapes of two-dimensional potential surfaces for the ground (X) and excited (B) states of HeCl2, binding energies De with respect to He+Cl2, stretching and bending vibrational frequencies of the complex, binding energies D0, and spectral shifts for the B←X transition are discussed.
Ion-neutral potential models in atmospheric pressure ion mobility time-of-flight mass spectrometry IM(tof)MS.

PubMed

Steiner, Wes E; English, William A; Hill, Herbert H

2006-02-09

The ion mobilities and their respective masses of several classes of amines (primary, secondary, and tertiary) were measured by electrospray ionization atmospheric pressure ion mobility time-of-flight mass spectrometry IM(tof)MS. The experimental data obtained were comparatively analyzed by the one-temperature kinetic theory of Chapman-Enskog. Several theoretical models were used to estimate the collision cross-sections; they include the rigid-sphere, polarization-limit, 12-6-4, and 12-4 potential models. These models were investigated to represent the interaction potentials contained within the collision integral that occurs between the polyatomic ions and the neutral drift gas molecules. The effectiveness of these collision cross-section models on predicting the mobility of these amine ions was explored. Moreover, the effects of drift gas selectivity on the reduced-mass term and in the collision cross-section term was examined. Use of a series of drift gases, namely, helium, neon, argon, nitrogen, and carbon dioxide, made it possible to distinguish between mass effects and polarizability effects. It was found that the modified 12-4 potential that compensates for the center of charge not being at the same location as the centers of mass showed improved agreement over the other collision cross-section models with respect to experimental data.
Consistent post-reaction vibrational energy redistribution in DSMC simulations using TCE model

NASA Astrophysics Data System (ADS)

Borges Sebastião, Israel; Alexeenko, Alina

2016-10-01

The direct simulation Monte Carlo (DSMC) method has been widely applied to study shockwaves, hypersonic reentry flows, and other nonequilibrium flow phenomena. Although there is currently active research on high-fidelity models based on ab initio data, the total collision energy (TCE) and Larsen-Borgnakke (LB) models remain the most often used chemistry and relaxation models in DSMC simulations, respectively. The conventional implementation of the discrete LB model, however, may not satisfy detailed balance when recombination and exchange reactions play an important role in the flow energy balance. This issue can become even more critical in reacting mixtures involving polyatomic molecules, such as in combustion. In this work, this important shortcoming is addressed and an empirical approach to consistently specify the post-reaction vibrational states close to thermochemical equilibrium conditions is proposed within the TCE framework. Following Bird's quantum-kinetic (QK) methodology for populating post-reaction states, the new TCE-based approach involves two main steps. The state-specific TCE reaction probabilities for a forward reaction are first pre-computed from equilibrium 0-D simulations. These probabilities are then employed to populate the post-reaction vibrational states of the corresponding reverse reaction. The new approach is illustrated by application to exchange and recombination reactions relevant to H2-O2 combustion processes.
Nature of bonding and cooperativity in linear DMSO clusters: A DFT, AIM and NCI analysis.

PubMed

Venkataramanan, Natarajan Sathiyamoorthy; Suvitha, Ambigapathy

2018-05-01

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

NASA Astrophysics Data System (ADS)

Wakabayashi, Tomonari; Wada, Yoriko; Iwahara, Naoya; Sato, Tohru

2013-04-01

Hydrogen-capped linear carbon chain molecules, namely polyynes H(C≡C)nH (n>=2), give rise to three excited states in the HOMO-LUMO excitation. Electric dipole transition from the ground state is fully allowed to one of the three excited states, while forbidden for the other two low-lying excited states. In addition to the strong absorption bands in the UV for the allowed transition, the molecules exhibit weak absorption and emission bands in the near UV and visible wavelength regions. The weak features are the vibronic bands in the forbidden transition. In this article, symmetry considerations are presented for the optical transitions in the centrosymmetric linear polyyne molecule. The argument includes Herzberg-Teller expansion for the state mixing induced by nuclear displacements along the normal coordinate of the molecule, intensity borrowing from fully allowed transitions, and inducing vibrational modes excited in the vibronic transition. The vibronic coupling considered here includes off-diagonal matrix elements for second derivatives along the normal coordinate. The vibronic selection rule for the forbidden transition is derived and associated with the transition moment with respect to the molecular axis. Experimental approaches are proposed for the assignment of the observed vibronic bands.
The complete mitochondrial genome of Hydra vulgaris (Hydroida: Hydridae).

PubMed

Pan, Hong-Chun; Fang, Hong-Yan; Li, Shi-Wei; Liu, Jun-Hong; Wang, Ying; Wang, An-Tai

2014-12-01

The complete mitochondrial genome of Hydra vulgaris (Hydroida: Hydridae) is composed of two linear DNA molecules. The mitochondrial DNA (mtDNA) molecule 1 is 8010 bp long and contains six protein-coding genes, large subunit rRNA, methionine and tryptophan tRNAs, two pseudogenes consisting respectively of a partial copy of COI, and terminal sequences at two ends of the linear mtDNA, while the mtDNA molecule 2 is 7576 bp long and contains seven protein-coding genes, small subunit rRNA, methionine tRNA, a pseudogene consisting of a partial copy of COI and terminal sequences at two ends of the linear mtDNA. COI gene begins with GTG as start codon, whereas other 12 protein-coding genes start with a typical ATG initiation codon. In addition, all protein-coding genes are terminated with TAA as stop codon.
Study of the In2O3 molecule in the free state and in the crystal

NASA Astrophysics Data System (ADS)

Kaplan, Ilya G.; Miranda, Ulises; Trakhtenberg, Leonid I.

2018-03-01

The nanomaterials based on the In2O3 molecule are widely used as catalysts and sensors among other applications. In the present study, we discuss the possibility of using nanoclusters of In2O3 as molecular photomotors. A comparative analysis of the electronic structure of the In2O3 molecule in the free state and in the crystal is performed. For the free In2O3 molecule the geometry of its lowest structures, V-shape and linear, was optimised at the CCSD(T) level, which is the most precise computational method applied up to date to study In2O3. Using experimental crystallographic data, we determined the geometry of In2O3 in the crystal. It has a zigzag, not symmetric structure and possesses a dipole moment with magnitude slightly smaller than that of the V-structure of the free molecule (the linear structure due to its symmetry has no dipole moment). According to the Natural Atomic population analysis, the chemical structure of the linear In2O3 can be represented as O = In-O-In = O; the V-shaped molecule has the similar double- and single-bond structure. The construction of nanoclusters from ´bricksʼ of In2O3 with geometry extracted from crystal (or nanoclusters extracted directly from crystal) and their use as photo-driven molecular motors are discussed.
Simulation of size-exclusion chromatography distribution coefficients of comb-shaped molecules in spherical pores comparison of simulation and experiment.

PubMed

Radke, Wolfgang

2004-03-05

Simulations of the distribution coefficients of linear polymers and regular combs with various spacings between the arms have been performed. The distribution coefficients were plotted as a function of the number of segments in order to compare the size exclusion chromatography (SEC)-elution behavior of combs relative to linear molecules. By comparing the simulated SEC-calibration curves it is possible to predict the elution behavior of comb-shaped polymers relative to linear ones. In order to compare the results obtained by computer simulations with experimental data, a variety of comb-shaped polymers varying in side chain length, spacing between the side chains and molecular weights of the backbone were analyzed by SEC with light-scattering detection. It was found that the computer simulations could predict the molecular weights of linear molecules having the same retention volume with an accuracy of about 10%, i.e. the error in the molecular weight obtained by calculating the molecular weight of the comb-polymer based on a calibration curve constructed using linear standards and the results of the computer simulations are of the same magnitude as the experimental error of absolute molecular weight determination.
Li2O (LiOLi)

NASA Astrophysics Data System (ADS)

Guelachvili, G.

This document is part of Subvolume B `Linear Triatomic Molecules', Part 9, of Volume 20 `Molecular Constants mostly from Infrared Spectroscopy' of Landolt-Börnstein Group II `Molecules and Radicals'.
Effects of monohydric alcohols and polyols on the thermal stability of a protein

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

Murakami, Shota; Kinoshita, Masahiro, E-mail: kinoshit@iae.kyoto-u.ac.jp

2016-03-28

The thermal stability of a protein is lowered by the addition of a monohydric alcohol, and this effect becomes larger as the size of hydrophobic group in an alcohol molecule increases. By contrast, it is enhanced by the addition of a polyol possessing two or more hydroxyl groups per molecule, and this effect becomes larger as the number of hydroxyl groups increases. Here, we show that all of these experimental observations can be reproduced even in a quantitative sense by rigid-body models focused on the entropic effect originating from the translational displacement of solvent molecules. The solvent is either puremore » water or water-cosolvent solution. Three monohydric alcohols and five polyols are considered as cosolvents. In the rigid-body models, a protein is a fused hard spheres accounting for the polyatomic structure in the atomic detail, and the solvent is formed by hard spheres or a binary mixture of hard spheres with different diameters. The effective diameter of cosolvent molecules and the packing fractions of water and cosolvent, which are crucially important parameters, are carefully estimated using the experimental data of properties such as the density of solid crystal of cosolvent, parameters in the pertinent cosolvent-cosolvent interaction potential, and density of water-cosolvent solution. We employ the morphometric approach combined with the integral equation theory, which is best suited to the physical interpretation of the calculation result. It is argued that the degree of solvent crowding in the bulk is the key factor. When it is made more serious by the cosolvent addition, the solvent-entropy gain upon protein folding is magnified, leading to the enhanced thermal stability. When it is made less serious, the opposite is true. The mechanism of the effects of monohydric alcohols and polyols is physically the same as that of sugars. However, when the rigid-body models are employed for the effect of urea, its addition is predicted to enhance the thermal stability, which conflicts with the experimental fact. We then propose, as two essential factors, not only the solvent-entropy gain but also the loss of protein-solvent interaction energy upon protein folding. The competition of changes in these two factors induced by the cosolvent addition determines the thermal-stability change.« less
Effects of monohydric alcohols and polyols on the thermal stability of a protein

NASA Astrophysics Data System (ADS)

Murakami, Shota; Kinoshita, Masahiro

2016-03-01

The thermal stability of a protein is lowered by the addition of a monohydric alcohol, and this effect becomes larger as the size of hydrophobic group in an alcohol molecule increases. By contrast, it is enhanced by the addition of a polyol possessing two or more hydroxyl groups per molecule, and this effect becomes larger as the number of hydroxyl groups increases. Here, we show that all of these experimental observations can be reproduced even in a quantitative sense by rigid-body models focused on the entropic effect originating from the translational displacement of solvent molecules. The solvent is either pure water or water-cosolvent solution. Three monohydric alcohols and five polyols are considered as cosolvents. In the rigid-body models, a protein is a fused hard spheres accounting for the polyatomic structure in the atomic detail, and the solvent is formed by hard spheres or a binary mixture of hard spheres with different diameters. The effective diameter of cosolvent molecules and the packing fractions of water and cosolvent, which are crucially important parameters, are carefully estimated using the experimental data of properties such as the density of solid crystal of cosolvent, parameters in the pertinent cosolvent-cosolvent interaction potential, and density of water-cosolvent solution. We employ the morphometric approach combined with the integral equation theory, which is best suited to the physical interpretation of the calculation result. It is argued that the degree of solvent crowding in the bulk is the key factor. When it is made more serious by the cosolvent addition, the solvent-entropy gain upon protein folding is magnified, leading to the enhanced thermal stability. When it is made less serious, the opposite is true. The mechanism of the effects of monohydric alcohols and polyols is physically the same as that of sugars. However, when the rigid-body models are employed for the effect of urea, its addition is predicted to enhance the thermal stability, which conflicts with the experimental fact. We then propose, as two essential factors, not only the solvent-entropy gain but also the loss of protein-solvent interaction energy upon protein folding. The competition of changes in these two factors induced by the cosolvent addition determines the thermal-stability change.
Trace element analysis of human urine collected after administration of Gd-based MRI contrast agents: characterizing spectral interferences using inorganic mass spectrometry

PubMed Central

Steuerwald, Amy J.; Parsons, Patrick J.; Arnason, John G.; Chen, Zhen; Peterson, C. Matthew; Louis, Germaine M. Buck

2013-01-01

Analysis of human urine is commonly used in biomonitoring studies to assess exposure to essential (e.g., Cu, Zn, Se) and non-essential (Pb, Cd, Pt) trace elements. These data are also used in epidemiological studies to evaluate potential associations between trace element exposure and various health outcomes within a population. Today most trace element analyses are typically performed using quadrupole-based inductively coupled plasma mass spectrometry (Q-ICP-MS). However, there is always the potential for spectral interferences with Q-ICP-MS instrumentation, especially when analyzing human specimens that may contain medications and other exogenous substances. Moreover, such xenobiotics may be unknown to the investigators. In a recent study focusing on environmental exposures and endometriosis: Endometriosis: Natural History, Diagnosis, and Outcomes (ENDO Study), urine specimens (n=619) were collected from participating women upon enrollment into the study or prior to surgery or pelvic magnetic resonance imaging (MRI), and analyzed for 21 trace elements by Q-ICP-MS. Here we report on some anomalous results observed for Se and Pt with elevated concentrations up to several orders of magnitude greater than what might be expected based on established reference intervals. Further investigations using Sector Field (SF-) ICP-MS instrumentation led to identification of doubly charged and polyatomic gadolinium (Gd) species traced to a Gd-based contrast agent that was administered to some subjects just prior to urine collection. Specifically, interferences from Gd2+ and several minor polyatomics were identified as interferences on all of the major isotopes of Se including 74Se, 76Se, 77Se, 78Se, 80Se, and 82Se. While trace amounts of Pt were present in the urine, a number of Gd-containing polyatomic species were also evident as major interferences on all isotopes of Pt (190Pt, 192Pt, 194Pt, 195Pt, 196Pt, and 198Pt), including Gd-chlorides, Gd-argides, and Gd-oxides. These observations underscore the importance of considering potential isobaric interferences when interpreting unusual trace element results for clinical specimens. PMID:27397951
Proton affinities of hydrated molecules

NASA Astrophysics Data System (ADS)

Valadbeigi, Younes

2016-09-01

Proton affinities (PA) of non-hydrated, M, and hydrated forms, M(H2O)1,2,3, of 20 organic molecules including alcohols, ethers, aldehydes, ketones and amines were calculated by the B3LYP/6-311++G(d,p) method. For homogeneous families, linear correlations were observed between PAs of the M(H2O)1,2,3 and the PAs of the non-hydrated molecules. Also, the absolute values of the hydration enthalpies of the protonated molecules decreased linearly with the PAs. The correlation functions predicted that for an amine with PA < 1100 kJ/mol the PA(M(H2O)) is larger than the corresponding PA, while for an amine with PA > 1100 kJ/mol the PA(M(H2O)) is smaller than the PA.
Packing C60 in Boron Nitride Nanotubes

NASA Astrophysics Data System (ADS)

Mickelson, W.; Aloni, S.; Han, Wei-Qiang; Cumings, John; Zettl, A.

2003-04-01

We have created insulated C60 nanowire by packing C60 molecules into the interior of insulating boron nitride nanotubes (BNNTs). For small-diameter BNNTs, the wire consists of a linear chain of C60 molecules. With increasing BNNT inner diameter, unusual C60 stacking configurations are obtained (including helical, hollow core, and incommensurate) that are unknown for bulk or thin-film forms of C60. C60 in BNNTs thus presents a model system for studying the properties of dimensionally constrained ``silo'' crystal structures. For the linear-chain case, we have fused the C60 molecules to form a single-walled carbon nanotube inside the insulating BNNT.
Dynamics of a linear magnetic “microswimmer molecule”

NASA Astrophysics Data System (ADS)

Babel, S.; Löwen, H.; Menzel, A. M.

2016-03-01

In analogy to nanoscopic molecules that are composed of individual atoms, we consider an active “microswimmer molecule”. It is made of three individual magnetic colloidal microswimmers that are connected by harmonic springs and interact hydrodynamically. In the ground state, they form a linear straight molecule. We analyze the relaxation dynamics for perturbations of this straight configuration. As a central result, with increasing self-propulsion, we observe an oscillatory instability in accord with a subcritical Hopf bifurcation scenario. It is accompanied by a corkscrew-like swimming trajectory of increasing radius. Our results can be tested experimentally, using, for instance, magnetic self-propelled Janus particles, supposably linked by DNA molecules.
The Dynamics of Entangled DNA Networks using Single-Molecule Methods

NASA Astrophysics Data System (ADS)

Chapman, Cole David

Single molecule experiments were performed on DNA, a model polymer, and entangled DNA networks to explore diffusion within complex polymeric fluids and their linear and non-linear viscoelasticity. DNA molecules of varying length and topology were prepared using biological methods. An ensemble of individual molecules were then fluorescently labeled and tracked in blends of entangled linear and circular DNA to examine the dependence of diffusion on polymer length, topology, and blend ratio. Diffusion was revealed to possess a non-monotonic dependence on the blend ratio, which we believe to be due to a second-order effect where the threading of circular polymers by their linear counterparts greatly slows the mobility of the system. Similar methods were used to examine the diffusive and conformational behavior of DNA within highly crowded environments, comparable to that experienced within the cell. A previously unseen gamma distributed elongation of the DNA in the presence of crowders, proposed to be due to entropic effects and crowder mobility, was observed. Additionally, linear viscoelastic properties of entangled DNA networks were explored using active microrheology. Plateau moduli values verified for the first time the predicted independence from polymer length. However, a clear bead-size dependence was observed for bead radii less than ~3x the tube radius, a newly discovered limit, above which microrheology results are within the continuum limit and may access the bulk properties of the fluid. Furthermore, the viscoelastic properties of entangled DNA in the non-linear regime, where the driven beads actively deform the network, were also examined. By rapidly driving a bead through the network utilizing optical tweezers, then removing the trap and tracking the bead's subsequent motion we are able to model the system as an over-damped harmonic oscillator and find the elasticity to be dominated by stress-dependent entanglements.
The characteristics of polyimide photoalignment layer with chalcone derivatives produced by linear polarized UV light

NASA Astrophysics Data System (ADS)

Jung, Kyoung Hoon; Hyun, Soon-Young; Song, Dong-Mee; Shin, Dong-Myung

2003-01-01

The photoalignment of liquid crystal (LC) molecules located onto polyimide films with chalcone derivatives using linearly polarized UV (LPUV) light is investigated. The LPUV light irradiation generated dimerization products of the chalcones followed by isomerization of the chalcone derivatives. The alignment directions of LC molecules were either homeotropic or planar with respect to plane of polyimide film, depending upon the alkyl chain length attached on the chalcones.
3' Homologous Free Ends are Required for Stable Joint Molecule Formation by the RecA and Single-Stranded Binding Proteins of Escherichia coli

NASA Astrophysics Data System (ADS)

Konforti, Boyana B.; Davis, Ronald W.

1987-02-01

The RecA protein of Escherichia coli is important for genetic recombination in vivo and can promote synapsis and strand exchange in vitro. The DNA pairing and strand exchange reactions have been well characterized in reactions with circular single strands and linear duplexes, but little is known about these two processes using substrates more characteristic of those likely to exist in the cell. Single-stranded linear DNAs were prepared by separating strands of duplex molecules or by cleaving single-stranded circles at a unique restriction site created by annealing a short defined oligonucleotide to the circle. Analysis by gel electrophoresis and electron microscopy revealed that, in the presence of RecA and single-stranded binding proteins, a free 3' homologous end is essential for stable joint molecule formation between linear single-stranded and circular duplex DNA.
Molecular t-matrices for Low-Energy Electron Diffraction (TMOL v1.1)

NASA Astrophysics Data System (ADS)

Blanco-Rey, Maria; de Andres, Pedro; Held, Georg; King, David A.

2004-08-01

We describe a FORTRAN-90 program that computes scattering t-matrices for a molecule. These can be used in a Low-Energy Electron Diffraction program to solve the molecular structural problem very efficiently. The intramolecular multiple scattering is computed within a Dyson-like approach, using free space Green propagators in a basis of spherical waves. The advantage of this approach is related to exploiting the chemical identity of the molecule, and to the simplicity to translate and rotate these t-matrices without performing a new multiple-scattering calculation for each configuration. FORTRAN-90 routines for rotating the resulting t-matrices using Wigner matrices are also provided. Program summaryTitle of program: TMOL Catalogue number: ADUF Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUF Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland. Computers: Alpha ev6-21264 (700 MHz) and Pentium-IV. Operating systems: Digital UNIX V5.0 and Linux (Red Hat 8.0). Programming language: FORTRAN-90/95 (Compaq True64 compiler, and Intel Fortran Compiler 7.0 for Linux). High-speed storage required for the test run: minimum 64 Mbytes, it can grow to more depending on the system considered. Disk storage required: None. No. of bits in a word: 64 and 32. No. of lines in distributed program, including test data etc.: 5404 No. of bytes in distributed program, including test data etc.: 59 856 Distribution format: tar.gz Nature of problem: We describe the FORTRAN-90 program TMOL (v1.1) for the computation of non-diagonal scattering t-matrices for molecules or any other poly-atomic sub-unit of surface structures. These matrices can be used in an standard Low-Energy Electron Diffraction program, such as LEED90 or CLEED. Method of solution: A general non-diagonal t-matrix is assumed for the atoms or more general scatterers forming the molecule. The molecular t-matrix is solved adding the possible intramolecular multiple scattering events using Green's propagator formalism. The resulting t-matrix is referred to the mass centre of the molecule and can be easily translated with these propagators and rotated applying Wigner matrices. Typical running time: Calculating the t-matrix for a single energy takes a few seconds. Time depends on the maximum angular momentum quantum number, lmax, and the number of scatterers in the molecule, N. Running time scales as lmax6 and N3. References: [1] S. Andersson, J.B. Pendry, J. Phys. C: Solid St. Phys. 13 (1980) 3547. [2] A. Gonis, W.H. Butler, Multiple Scattering in Solids, Springer-Verlag, Berlin/New York, 2000.

The Optical Spectrum of SrOH Re-Visited Zeeman Effect, High-Resolution Spectroscopy and Franck-Condon Factors.

NASA Astrophysics Data System (ADS)

Nguyen, Trung; Kokkin, Damian L.; Steimle, Timothy; Kozyryev, Ivan; Doyle, John M.

2015-06-01

Motivated by a diverse range of applications in physics and chemistry, currently there is great interest in the cooling of molecules to very low temperatures (≤1 mK). Direct laser cooling has been previously demonstrated for the diatomic radicals SrF, YO, and CaF, and most recently a three-dimensional magneto-optical trap (MOT) of SrF molecules was achieved. To determine the possibility of laser cooling for polyatomic molecules containing three or more atoms, detailed information is required about their Franck-Condon factors (FCFs) for emission from the excited states of interest. Here we report on the high-resolution laser excitation spectra, recorded field-free and in the presence of a static magnetic field, and on the dispersed fluorescence (DF) spectra for the A^2Π1/2 ← X^2σ^+ and B^2σ^+ ← X ^2σ^+ electronic transitions of SrOH. The DF spectra were analyzed to precisely determine FCFs and compared with values predicted using a normal coordinate GF matrix approach. The recorded Zeeman spectra were analyzed to determine the magnetic moments. Implication for proposed laser cooling and trapping experiments for SrOH will be presented. E.S. Shuman, J.F. Barry and D. DeMille, Nature 467, 820 (2010) J.F. Barry, E.S. Shuman, E.B. Norrgard and D. DeMille, Phys. Rev. Lett. 108, 103002 (2012) M.T. Hummon, M. Yeo, B.K. Stuhl, A.L. Collopy, Y. Xia, and J. Ye, Phys. Rev. Lett. 110, 143001 (2013) M. Yeo, M.T. Hummon, A.L. Collopy, B. Yan, B. Hemmerling, E. Chae, J.M. Doyle, and J. Ye, arXiv:1501.04683 (2015) V. Zhelyazkova, A. Cournol, T.E. Wall, A. Matsushima, J.J. Hudson, E.A. Hinds, M.R. Tarbutt, and B.E. Sauer, Phys. Rev. A 89, 053416 (2014) J.F. Barry, D.J. McCarron, E.B. Norrgard, M.H. Steinecker and D. DeMille, Nature 512, 286 (2014) D.J. McCarron, E.B. Norrgard, M.H. Steinecker and D. DeMille, arXiv:1412.8220 (2014)
Gyration-radius dynamics in structural transitions of atomic clusters.

PubMed

Yanao, Tomohiro; Koon, Wang S; Marsden, Jerrold E; Kevrekidis, Ioannis G

2007-03-28

This paper is concerned with the structural transition dynamics of the six-atom Morse cluster with zero total angular momentum, which serves as an illustrative example of the general reaction dynamics of isolated polyatomic molecules. It develops a methodology that highlights the interplay between the effects of the potential energy topography and those of the intrinsic geometry of the molecular internal space. The method focuses on the dynamics of three coarse variables, the molecular gyration radii. By using the framework of geometric mechanics and hyperspherical coordinates, the internal motions of a molecule are described in terms of these three gyration radii and hyperangular modes. The gyration radii serve as slow collective variables, while the remaining hyperangular modes serve as rapidly oscillating "bath" modes. Internal equations of motion reveal that the gyration radii are subject to two different kinds of forces: One is the ordinary force that originates from the potential energy function of the system, while the other is an internal centrifugal force. The latter originates from the dynamical coupling of the gyration radii with the hyperangular modes. The effects of these two forces often counteract each other: The potential force generally works to keep the internal mass distribution of the system compact and symmetric, while the internal centrifugal force works to inflate and elongate it. Averaged fields of these two forces are calculated numerically along a reaction path for the structural transition of the molecule in the three-dimensional space of gyration radii. By integrating the sum of these two force fields along the reaction path, an effective energy curve is deduced, which quantifies the gross work necessary for the system to change its mass distribution along the reaction path. This effective energy curve elucidates the energy-dependent switching of the structural preference between symmetric and asymmetric conformations. The present methodology should be of wide use for the systematic reduction of dimensionality as well as for the identification of kinematic barriers associated with the rearrangement of mass distribution in a variety of molecular reaction dynamics in vacuum.
Gyration-radius dynamics in structural transitions of atomic clusters

NASA Astrophysics Data System (ADS)

Yanao, Tomohiro; Koon, Wang S.; Marsden, Jerrold E.; Kevrekidis, Ioannis G.

2007-03-01

This paper is concerned with the structural transition dynamics of the six-atom Morse cluster with zero total angular momentum, which serves as an illustrative example of the general reaction dynamics of isolated polyatomic molecules. It develops a methodology that highlights the interplay between the effects of the potential energy topography and those of the intrinsic geometry of the molecular internal space. The method focuses on the dynamics of three coarse variables, the molecular gyration radii. By using the framework of geometric mechanics and hyperspherical coordinates, the internal motions of a molecule are described in terms of these three gyration radii and hyperangular modes. The gyration radii serve as slow collective variables, while the remaining hyperangular modes serve as rapidly oscillating "bath" modes. Internal equations of motion reveal that the gyration radii are subject to two different kinds of forces: One is the ordinary force that originates from the potential energy function of the system, while the other is an internal centrifugal force. The latter originates from the dynamical coupling of the gyration radii with the hyperangular modes. The effects of these two forces often counteract each other: The potential force generally works to keep the internal mass distribution of the system compact and symmetric, while the internal centrifugal force works to inflate and elongate it. Averaged fields of these two forces are calculated numerically along a reaction path for the structural transition of the molecule in the three-dimensional space of gyration radii. By integrating the sum of these two force fields along the reaction path, an effective energy curve is deduced, which quantifies the gross work necessary for the system to change its mass distribution along the reaction path. This effective energy curve elucidates the energy-dependent switching of the structural preference between symmetric and asymmetric conformations. The present methodology should be of wide use for the systematic reduction of dimensionality as well as for the identification of kinematic barriers associated with the rearrangement of mass distribution in a variety of molecular reaction dynamics in vacuum.
Comprehensive mass spectrometric analysis of novel organic semiconductor molecules

NASA Astrophysics Data System (ADS)

Prada, Svitlana

This work presents a comprehensive mass spectrometry (MS) study of novel organic semiconductor molecules including ion mobility/reactivity measurements and trace elemental analysis. The organic molecules investigated here are important semiconductor materials for molecular electronic devices such as Organic Field-Effect Transistors (OFETs) and Light Emitted Diodes (LED). A high-performance orthogonal time-of flight mass spectrometer (TOF-MS) in combination with a matrix assisted laser desorption/ionization (MALDI) source operating at elevated pressure was used to perform MALDI/TOF analyses of pentacene and some of its derivatives with and without an added matrix. The observation of ion-molecule reactions between "cold" analyte ions and neutral analyte molecules in the gas phase has provided some insight into the mechanism of pentacene cluster formation and its functionalized derivatives. Furthermore, some of the matrices employed to assist the desorption/ionization process of these compounds were observed to influence the outcome via ion-molecule reactions of analyte ions and matrix molecules in the gas phase. The stability and reactivity of the compounds and their clusters in the MALDI plume during gas-phase expansion were evaluated; possible structures of the resulting clusters are discussed. The MALDI/TOF technique was also helpful in distinguishing between two isomeric forms of bis-[(triisopropylsilyl)-ethynyl]-pentacene. Furthermore, we reported ion mobility measurements of functionalized pentacene ions with a modified triple quadrupole mass spectrometer fitted with an ion molecule reactor (IMR). The IMR is equipped with a variable axial electrostatic drift field (ADF) and is able to trap ions for a prolong period of time. These capabilities were successfully employed in the measurement of ion mobilities in different modes of the IMR operation. Theoretical modeling of the drift dynamics and the special localization of the large ion packet was successfully implemented. The contribution of the quadrupole RF field to the drift dynamics also was taken into consideration. The IMR was successfully employed in the ion-molecule reactions study of four functionalized pentacene derivatives such as TIPS, o-TIPS, 6,13-bis-[(triisopropylsilyl)-ethynyl]-pentacene-2,3-dicarbonitrile (TIPS(CN)2), and 6,13-bis-[(triisopropylsilyl)-ethynyl]-pentacene-2,3,9,10-tetracarbonitrile (TIPS(CN)4). Details of the IMR operation in this mode are extensively discussed. The purity of the starting material is one of the most important parameters for the fabrication of a molecular electronic device. We report the method of determination of trace elemental impurities (Li, Na, Al, Mg, Be, Pb, Mn, Co, Ti, Sn, Cu, Cr, V, Zn, Fe, Ca, K and Ni) in organic semiconductor materials, such as Tetracene, Anthracene, Pentacene, TIPS and Rubrene, using an inductively coupled plasma quadrupole mass spectrometer (ICP-MS) fitted with a dynamic reaction cell (DRC). The determination of Fe, Ca, K and Ni in the organic semiconductor materials was carried out using NH3 as a reaction gas in the DRC mode to obviate the effect of polyatomic isobaric interferences. The other trace elements such as Li, Na, Al, Mg, Be, Pb, Mn, Co, Ti, Sn, Cu, Cr, V and Zn have been determined under standard operating conditions.
Energy Level Alignment at the Interface between Linear-Structured Benzenediamine Molecules and Au(111) Surface

NASA Astrophysics Data System (ADS)

Li, Guo; Rangel, Tonatiuh; Liu, Zhenfei; Cooper, Valentino; Neaton, Jeffrey

Using density functional theory with model self-energy corrections, we calculate the adsorption energetics and geometry, and the energy level alignment of benzenediamine (BDA) molecules adsorbed on Au(111) surfaces. Our calculations show that linear structures of BDA, stabilized via hydrogen bonds between amine groups, are energetically more favorable than monomeric phases. Moreover, our self-energy-corrected calculations of energy level alignment show that the highest occupied molecular orbital energy of the BDA linear structure is deeper relative to the Fermi level relative to the isolated monomer and agrees well with the values measured with photoemission spectroscopy. This work supported by DOE.
High-order harmonic generation of CO and N2 molecules under linearly- and bi circularly-polarized laser pulses by TD-DFT

NASA Astrophysics Data System (ADS)

Koushki, A. M.; Sadighi-Bonabi, R.; Mohsen-Nia, M.; Irani, E.

2018-07-01

We present a method for high-order harmonics generation of N2 and CO molecules under two-color circularly polarized counter-rotating laser pulses at frequencies of and 2. Pulse envelope in this investigation is sin-squared and the intensity of each laser beam is with ten-optical cycle (o.c.). We show that an isolated pulse with a pulse duration shorter than 20 attosecond from the superposition of several harmonics can be generated. Both two-color linearly- and bicircularly-polarized laser pulses are considered. Our results have also been compared with the outcomes of the previous theoretical works as well as experiment observations. It is found that for CO molecule, the bicircularly-polarized laser pulses are superior and more efficient, and it can generate narrower attosecond pulses than the linearly-polarized pulses. While for N2 molecule, the two-color linearly-polarized pulses are more efficient, and it can generate narrower attosecond pulses than the bicircularly-polarized pulses. Furthermore, in order to demonstrate the origin of red- and blue-shifts in high-harmonic spectra, the effect of pulse duration on the high-order harmonics spectra is investigated. In addition, to obtain imaging on the temporal dependence of the electron densities, the time dependent electron localization function is used. Moreover, in order to study of the quantum trajectory of electrons, time-frequency analysis is utilized.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

The following are reported: theoretical calculations (configuration interaction, relativistic effective core potentials, polyatomics, CASSCF); proposed theoretical studies (clusters of Cu, Ag, Au, Ni, Pt, Pd, Rh, Ir, Os, Ru; transition metal cluster ions; transition metal carbide clusters; bimetallic mixed transition metal clusters); reactivity studies on transition metal clusters (reactivity with H{sub 2}, C{sub 2}H{sub 4}, hydrocarbons; NO and CO chemisorption on surfaces). Computer facilities and codes to be used, are described. 192 refs, 13 figs.
Photodissociation Studies of Polyatomic Free Radicals

DTIC Science & Technology

1993-08-01

photofragment, that varies with vibrational level, and appears to have a strong J dependence. We are currently in the process of modelling these effects, as well...have also begun to study the photodissociation dynamics of thionyl halides, The photodissociation of thionyl chloride (C12SO) is of interest as a model ...concerted three-body fragmentation mechanism as the primary dissociation channel. A Franck- Condon/golden rule model elucidates the geometry prior to
A New Scaling Law of Resonance in Total Scattering Cross Section in Gases

NASA Astrophysics Data System (ADS)

Raju, Gorur Govinda

2009-10-01

Electrical discharges in gases continue to be an active area of research because of industrial applications such as power systems, environmental clean up, laser technology, semiconductor fabrication etc. A fundamental knowledge of electron-gas neutral interaction is indispensable and, the total scattering cross section is one of the quantities that have been measured extensively. The energy dependence of the total cross sections shows peaks or resonance processes that are operative in the collision process. These peaks and the energies at which they occur are shown to satisfy a broad relationship involving the polarizability and the dipole moment of the target particle. Data on 62 target particles belonging to the following species are analyzed. (Eq 1) Rare gas atoms (Eq 2) Di-atomic molecules with combinations of polar, non-polar, attaching, and non-attaching properties Poly-atomic molecules with combinations of polar, non-polar, attaching, and non-attaching properties. Methods of improving the newly identified scaling law and possible application have been identified. 1 INTRODUCTION: Data on electron-neutral interactions are one of the most fundamental in the study of gaseous electronics and an immense literature, both experimental and theoretical, has become available since about the year 1920. [1-5]. In view of the central role which these data play in all facets of gas discharges and plasma science, it is felt that a critical review of available data is timely, mainly for the community of high voltage engineers and industries connected with plasma science in general. The electron-neutral interaction, often referred to as scattering in the scientific literature, is quantified by using the quantity called the total scattering cross section (QT, m^2). In the literature on cross section, total cross section and total scattering cross section are terms used synonymously and we follow the same practice. A definition may be found in reference [1]. This paper concerns scaling of total cross section of gases at resonance energy and the electron energy at which resonance occurs. The meaning of resonance is briefly explained in the following section. Here, we use the term scaling to relate the two quantities mentioned, namely, the resonance energy and the total cross section at that energy. Consistent with the definition of scaling, if the law proposed holds, one of the two quantities mentioned above may be calculated if the other is known. Such a method is very useful in gas discharge modeling and calculation of breakdown voltages, as more fully explained in the later section of the paper. 2 DESCRIPTION OF RESONANCE: A brief description of resonance phenomena in several types of target particles, viz., atomic, poly atomic, polar, non-polar phenomena are presented. 3 PREVIOUS SCALING LAWS: A common representation of a given characteristic with as few adjustable parameters as possible is generally known as the scaling law. The Paschen curve for breakdown voltage is such a familiar scaling law. With reference to cross sections several attempts have been made to obtain a scaling law, with varying degree of success. If the cross section-energy curve is qualitatively similar without having sharp peaks and oscillations, moderately successful scaling laws may be devised. For example, the ionization cross section- energy curves for most gases follow a general pattern. Several published scaling laws are discussed. 4 A NEW SCALING LAW AND DISCUSSION: In this work the author has compiled the resonance details for more than 60 gasest hat include the range from simple atoms to complex molecules that are polyatomic, dipolar, electron-attaching and isomers. The target particles exhibit a number of distinct features, as far as their total cross section variation with electron energy is concerned as already explained.
Anisotropic contribution to the van der Waals and the Casimir-Polder energies for CO2 and CH4 molecules near surfaces and thin films

NASA Astrophysics Data System (ADS)

Thiyam, Priyadarshini; Parashar, Prachi; Shajesh, K. V.; Persson, Clas; Schaden, Martin; Brevik, Iver; Parsons, Drew F.; Milton, Kimball A.; Malyi, Oleksandr I.; Boström, Mathias

2015-11-01

In order to understand why carbon dioxide (CO2) and methane (CH4) molecules interact differently with surfaces, we investigate the Casimir-Polder energy of a linearly polarizable CO2 molecule and an isotropically polarizable CH4 molecule in front of an atomically thin gold film and an amorphous silica slab. We quantitatively analyze how the anisotropy in the polarizability of the molecule influences the van der Waals contribution to the binding energy of the molecule.
Covariance Matrix Estimation for the Cryo-EM Heterogeneity Problem*

PubMed Central

Katsevich, E.; Katsevich, A.; Singer, A.

2015-01-01

In cryo-electron microscopy (cryo-EM), a microscope generates a top view of a sample of randomly oriented copies of a molecule. The problem of single particle reconstruction (SPR) from cryo-EM is to use the resulting set of noisy two-dimensional projection images taken at unknown directions to reconstruct the three-dimensional (3D) structure of the molecule. In some situations, the molecule under examination exhibits structural variability, which poses a fundamental challenge in SPR. The heterogeneity problem is the task of mapping the space of conformational states of a molecule. It has been previously suggested that the leading eigenvectors of the covariance matrix of the 3D molecules can be used to solve the heterogeneity problem. Estimating the covariance matrix is challenging, since only projections of the molecules are observed, but not the molecules themselves. In this paper, we formulate a general problem of covariance estimation from noisy projections of samples. This problem has intimate connections with matrix completion problems and high-dimensional principal component analysis. We propose an estimator and prove its consistency. When there are finitely many heterogeneity classes, the spectrum of the estimated covariance matrix reveals the number of classes. The estimator can be found as the solution to a certain linear system. In the cryo-EM case, the linear operator to be inverted, which we term the projection covariance transform, is an important object in covariance estimation for tomographic problems involving structural variation. Inverting it involves applying a filter akin to the ramp filter in tomography. We design a basis in which this linear operator is sparse and thus can be tractably inverted despite its large size. We demonstrate via numerical experiments on synthetic datasets the robustness of our algorithm to high levels of noise. PMID:25699132
Remote Raman Efficiencies and Cross-Sections of Organic and Inorganic Chemicals.

PubMed

Acosta-Maeda, Tayro E; Misra, Anupam K; Porter, John N; Bates, David E; Sharma, Shiv K

2017-05-01

We determined Raman cross-sections of various organic liquids and inorganic polyatomic ions in aqueous solutions with a 532 nm pulsed laser using remote Raman systems developed at the University of Hawaii. Using a calibrated integrating sphere as a light source, we converted the intensity counts in the spectrum of the light from the integrating sphere measured with UH remote Raman instrument to spectral radiance. From these data, a response function of the remote Raman instrument was obtained. With the intensity-calibrated instrument, we collected remote Raman data from a standard 1 mm path length fused silica spectrophotometer cell filled with cyclohexane. The measured value of the differential Raman cross-section for the 801 cm -1 vibrational mode of cyclohexane is 4.55 × 10 -30 cm 2 sr -1 molecule -1 when excited by a 532 nm laser, in good agreement with the values reported in the literature. Using the measured cyclohexane Raman cross-section as a reference and relative Raman mode intensities of the various ions and organic liquids, we calculated the Raman cross-sections of the strongest Raman lines of nitrate, sulfate, carbonate, phosphate ions, and organic liquids by maintaining same experimental conditions for remote Raman detection. These relative Raman cross-section values will be useful for estimating detection capabilities of remote Raman systems for planetary exploration.
Mode-specific multi-channel dynamics of the F- + CHD2Cl reaction on a global ab initio potential energy surface

NASA Astrophysics Data System (ADS)

Szabó, István; Czakó, Gábor

2016-10-01

We report a detailed quasiclassical trajectory study for the dynamics of the ground-state and CH/CD stretching-excited F- + CHD2Cl(vCH/CD = 0, 1) → Cl- + CHD2F, HF + CD2Cl-, and DF + CHDCl- SN2, proton-, and deuteron-abstraction reactions using a full-dimensional global ab initio analytical potential energy surface. The simulations show that (a) CHD2Cl(vCH/CD = 1), especially for vCH = 1, maintains its mode-specific excited character prior to interaction, (b) the SN2 reaction is vibrationally mode-specific, (c) double inversion can occur and is enhanced upon CH/CD stretching excitations, (d) in the abstraction reactions the HF channel is preferred and the vCH/CD = 1 excitations significantly promote the HF/DF channels, (e) back-side rebound, back-side stripping, and front-side stripping are the dominant direct abstraction mechanisms based on correlated scattering- and attack-angle distributions, (f) the exact classical vibrational energy-based Gaussian binning (1GB) provides realistic mode-specific polyatomic product state distributions, (g) in the abstraction reactions CH and CD stretchings are not pure spectator modes and mainly ground-state products are produced, thus most of the initial energy transfers into product translation, and (h) the HF and DF product molecules are rotationally cold without any significant dependence on the reactant's and HF/DF vibrational states.
Computation of Electron Impact Ionization Cross sections of Iron Hydrogen Clusters - Relevance in Fusion Plasmas

NASA Astrophysics Data System (ADS)

Patel, Umang; Joshipura, K. N.

2017-04-01

Plasma-wall interaction (PWI) is one of the key issues in nuclear fusion research. In nuclear fusion devices, such as the JET tokamak or the ITER, first-wall materials will be directly exposed to plasma components. Erosion of first-wall materials is a consequence of the impact of hydrogen and its isotopes as main constituents of the hot plasma. Besides the formation of gas-phase atomic species in various charge states, di- and polyatomic molecular species are expected to be formed via PWI processes. These compounds may profoundly disturb the fusion plasma, may lead to unfavorable re-deposition of materials and composites in other areas of the vessel. Interaction between atoms, molecules as well transport of impurities are of interest for modelling of fusion plasma. Qion by electron impact are such process also important in low temperature plasma processing, astrophysics etc. We reported electron impact Qionfor iron hydrogen clusters, FeHn (n = 1 to 10) from ionization threshold to 2000 eV. A semi empirical approach called Complex Scattering Potential - Ionization Contribution (CSP-ic) has been employed for the reported calculation. In context of fusion relevant species Qion were reported for beryllium and its hydrides, tungsten and its oxides and cluster of beryllium-tungsten by Huber et al.. Iron hydrogen clusters are another such species whose Qion were calculated through DM and BEB formalisms, same has been compared with present calculations.
Development of Solid-State Nanopore Technology for Life Detection

NASA Technical Reports Server (NTRS)

Bywaters, K. B.; Schmidt, H.; Vercoutere, W.; Deamer, D.; Hawkins, A. R.; Quinn, R. C.; Burton, A. S.; Mckay, C. P.

2017-01-01

Biomarkers for life on Earth are an important starting point to guide the search for life elsewhere. However, the search for life beyond Earth should incorporate technologies capable of recognizing an array of potential biomarkers beyond what we see on Earth, in order to minimize the risk of false negatives from life detection missions. With this in mind, charged linear polymers may be a universal signature for life, due to their ability to store information while also inherently reducing the tendency of complex tertiary structure formation that significantly inhibit replication. Thus, these molecules are attractive targets for biosignature detection as potential "self-sustaining chemical signatures." Examples of charged linear polymers, or polyelectrolytes, include deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) as well as synthetic polyelectrolytes that could potentially support life, including threose nucleic acid (TNA) and other xenonucleic acids (XNAs). Nanopore analysis is a novel technology that has been developed for singlemolecule sequencing with exquisite single nucleotide resolution which is also well-suited for analysis of polyelectrolyte molecules. Nanopore analysis has the ability to detect repeating sequences of electrical charges in organic linear polymers, and it is not molecule- specific (i.e. it is not restricted to only DNA or RNA). In this sense, it is a better life detection technique than approaches that are based on specific molecules, such as the polymerase chain reaction (PCR), which requires that the molecule being detected be composed of DNA.
Evolution of Linear Mitochondrial Genomes in Medusozoan Cnidarians

PubMed Central

Kayal, Ehsan; Bentlage, Bastian; Collins, Allen G.; Pirro, Stacy; Lavrov, Dennis V.

2012-01-01

In nearly all animals, mitochondrial DNA (mtDNA) consists of a single circular molecule that encodes several subunits of the protein complexes involved in oxidative phosphorylation as well as part of the machinery for their expression. By contrast, mtDNA in species belonging to Medusozoa (one of the two major lineages in the phylum Cnidaria) comprises one to several linear molecules. Many questions remain on the ubiquity of linear mtDNA in medusozoans and the mechanisms responsible for its evolution, replication, and transcription. To address some of these questions, we determined the sequences of nearly complete linear mtDNA from 24 species representing all four medusozoan classes: Cubozoa, Hydrozoa, Scyphozoa, and Staurozoa. All newly determined medusozoan mitochondrial genomes harbor the 17 genes typical for cnidarians and map as linear molecules with a high degree of gene order conservation relative to the anthozoans. In addition, two open reading frames (ORFs), polB and ORF314, are identified in cubozoan, schyphozoan, staurozoan, and trachyline hydrozoan mtDNA. polB belongs to the B-type DNA polymerase gene family, while the product of ORF314 may act as a terminal protein that binds telomeres. We posit that these two ORFs are remnants of a linear plasmid that invaded the mitochondrial genomes of the last common ancestor of Medusozoa and are responsible for its linearity. Hydroidolinan hydrozoans have lost the two ORFs and instead have duplicated cox1 at each end of their mitochondrial chromosome(s). Fragmentation of mtDNA occurred independently in Cubozoa and Hydridae (Hydrozoa, Hydroidolina). Our broad sampling allows us to reconstruct the evolutionary history of linear mtDNA in medusozoans. PMID:22113796
Chain-Length-Dependent Exciton Dynamics in Linear Oligothiophenes Probed Using Ensemble and Single-Molecule Spectroscopy.

PubMed

Kim, Tae-Woo; Kim, Woojae; Park, Kyu Hyung; Kim, Pyosang; Cho, Jae-Won; Shimizu, Hideyuki; Iyoda, Masahiko; Kim, Dongho

2016-02-04

Exciton dynamics in π-conjugated molecular systems is highly susceptible to conformational disorder. Using time-resolved and single-molecule spectroscopic techniques, the effect of chain length on the exciton dynamics in a series of linear oligothiophenes, for which the conformational disorder increased with increasing chain length, was investigated. As a result, extraordinary features of the exciton dynamics in longer-chain oligothiophene were revealed. Ultrafast fluorescence depolarization processes were observed due to exciton self-trapping in longer and bent chains. Increase in exciton delocalization during dynamic planarization processes was also observed in the linear oligothiophenes via time-resolved fluorescence spectra but was restricted in L-10T because of its considerable conformational disorder. Exciton delocalization was also unexpectedly observed in a bent chain using single-molecule fluorescence spectroscopy. Such delocalization modulates the fluorescence spectral shape by attenuating the 0-0 peak intensity. Collectively, these results provide significant insights into the exciton dynamics in conjugated polymers.
Absolute measurements and certified reference material for iron isotopes using multiple-collector inductively coupled mass spectrometry.

PubMed

Zhou, Tao; Zhao, Motian; Wang, Jun; Lu, Hai

2008-01-01

Two enriched isotopes, 99.94 at.% 56Fe and 99.90 at.% 54Fe, were blended under gravimetric control to prepare ten synthetic isotope samples whose 56Fe isotope abundances ranged from 95% to 20%. For multiple-collector inductively coupled plasma mass spectrometry (MC-ICP-MS) measurements typical polyatomic interferences were removed by using Ar and H2 as collision gas and operating the MC-ICP-MS system in soft mode. Thus high-precision measurements of the Fe isotope abundance ratios were accomplished. Based on the measurement of the synthetic isotope abundance ratios by MC-ICP-MS, the correction factor for mass discrimination was calculated and the results were in agreement with results from IRMM014. The precision of all ten correction factors was 0.044%, indicating a good linearity of the MC-ICP-MS method for different isotope abundance ratio values. An isotopic reference material was certified under the same conditions as the instrument was calibrated. The uncertainties of ten correction factors K were calculated and the final extended uncertainties of the isotopic certified Fe reference material were 5.8363(37) at.% 54Fe, 91.7621(51) at.% 56Fe, 2.1219(23) at.% 57Fe, and 0.2797(32) at.% 58Fe.
Speciation and preservation of CrVI and CrIII in finished drinking water matrices using collision cell ion chromatography-inductively coupled plasma-mass spectrometry

EPA Science Inventory

The polyatomic background at the major isotope of Cr was evaluated as a function of collision cell gas flow rate using three different mobile phases. The stability of CrVI was evaluated as a function of solution pH using an enriched 53CrVI. The recovery was ≥ 95% at pH 7.8 but...
Features of nanostructures sputtering

NASA Astrophysics Data System (ADS)

Kapustin, S. N.; Matveev, V. I.; Eseev, M. K.

2017-09-01

The research of ion sputtering of nanoparticles is interesting both from the fundamental point of view - for researching the interior structure of nanoobjects, and the economical one - nanostructures often play the role of functional supplements in composite materials under the radiation pressure. This process should be taken into account while creating objects decorated by nanoclusters during ion implantation. Polyatomic clusters obtained as a result of ion bombing could be used as nanodisperse catalysts or quantum points.

Exploring Molecular Complexity of the Diffuse and Translucent Gas and PhotoDissociation Regions

NASA Astrophysics Data System (ADS)

McCarthy, Michael

This proposal requests funds to continue a laboratory program in close coordination with radio astronomical observations dedicated to the study of highly reactive polyatomic molecular ions in low density regions and photo-dissociation regions (PDRs). In doing so, the proposed studies will advance our understanding of the chemistry beyond light ions that have been observed so successfully in these regions with Herschel and recently extended with SOFIA, and thereby critically address a significant but unresolved question in molecular astronomy: Are larger molecules formed in a bottom-up or top-down chemistry? The rotational spectra of most new molecular ions will be detected in the laboratory in a resonant microwave cavity, followed either by microwave/millimeterwave double resonance or millimeter/THz absorption to better characterize their spectrum in bands covered by the heterodyne receivers HIFI on Herschel and GREAT on SOFIA. In collaboration with radioastronomer colleagues, we will search for the new ions in the published survey of the PDR region of the Orion Bar and archival data of other PDRs observed with the IRAM 30 m telescope; retrieve and analyze archival data from Herschel; and undertake searches for some of the new ions in PDRs and low density regions with SOFIA. This work will also have a strong bearing on proposed Early Release Science (ERS) observations of dense PDRs with the James Webb Space Telescope (JWST). The laboratory effort will build on previous work on molecular ions , specifically detection of the rotational spectra of a number of positive ions of astronomical interest such as H2NCO+, CCCH+, the cis- and trans isomers of HOSO+, HNCOH+, and H2CC(H)CNH+. We will focus our efforts on positive ions derived from closed-shell neutral molecules, radicals, and carbenes whose rotational spectra have been observed in our laboratory, and nearly all of which have also been identified in galactic molecular clouds. Examples of the ions we seek include polyatomic ions such as CN+, HCCCN+, HNCO+, c-C3H2+, etc. Collaborations with leading theoretical groups to accurately predict spectroscopic constants of the new ions will enhance the proposed laboratory investigations. Instrumental refinement will also be undertaken with particular emphasis on construction of a new cryogenically cooled ( 6 K) buffer gas cell. This ultra-sensitive instrument will possess a system temperature that is nearly 50 times lower than our most sensitive cavity spectrometer, and one close to the fundamental limit set by modern technology, thereby greatly enhancing our ability to detect elusive molecular ions that are produced in very low steady state concentrations. The essential capabilities of this instrument have already been demonstrated in collaborative investigations. Our laboratory program is well aligned with NASA's overall mission, because we seek to understand the role of the chemical bond on a cosmic scale and to provide a firm chemical foundation by which more complicated questions of biological origins can be addressed. The work here also provides much basic information to aid subsequent astronomical searches, particularly in the infrared. Finally, our research program is an excellent vehicle for integrating research and education. It provides exposure to quite diverse areas of science in a setting which encourages student initiative and independent investigation.
Computer program to simulate Raman scattering

NASA Technical Reports Server (NTRS)

Zilles, B.; Carter, R.

1977-01-01

A computer program is described for simulating the vibration-rotation and pure rotational spectrum of a combustion system consisting of various diatomic molecules and CO2 as a function of temperature and number density. Two kinds of spectra are generated: a pure rotational spectrum for any mixture of diatomic and linear triatomic molecules, and a vibrational spectrum for diatomic molecules. The program is designed to accept independent rotational and vibrational temperatures for each molecule, as well as number densities.
FTIR Rotational Spectroscopy.

ERIC Educational Resources Information Center

Woods, Ron; Henderson, Giles

1987-01-01

Presented are representative examples of the spectra and the analyses for a linear molecule (HC1), a symmetric top molecule (NH3), and an asymmetric top (H2O). Any combination of these projects could be incorporated in a physical chemistry or molecular spectroscopy laboratory. (RH)
Classroom Demonstrations of Polymer Principles Part II. Polymer Formation.

ERIC Educational Resources Information Center

Rodriguez, F.; And Others

1987-01-01

This is part two in a series on classroom demonstrations of polymer principles. Described is how large molecules can be assembled from subunits (the process of polymerization). Examples chosen include both linear and branched or cross-linked molecules. (RH)
N(2)O in small para-hydrogen clusters: Structures and energetics.

PubMed

Zhu, Hua; Xie, Daiqian

2009-04-30

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

NASA Astrophysics Data System (ADS)

Blain, Matthew Glenn

1990-01-01

A new experimental method has been developed for studying negative secondary ion (SI) emission from solid surfaces bombarded by polyatomic primary ions of 5 to 30 keV. The method is based on the time-of-flight (TOF) analysis of primary ions which are produced by either ^ {252}Cf fission fragment induced desorption or by extraction from a liquid metal ion source, and then accelerated into a field free region. The primary ions included organic monomer, dimer, and fragment ions of coronene and phenylalanine, (CsI)_ nCs ^{+} cluster ions, and Au _sp{n}{+} cluster ions. Secondary electrons, emitted from a target surface upon primary ion impact, are used to identify which primary ion has hit the surface. An event-by-event coincidence counting technique allows several secondary ion TOF spectra, correlated to several different primary ions, to be acquired simultaneously. Negative SI yields from organic (phenylalanine and dinitrostilbene), CsI, and Au surfaces have been measured for a number of different mono- and polyatomic primary ions. The results show, for example, yields ranging from 1 to 10% for phenylalanine (M-H) ^{ -}, 1 to 10% for I^{-} , and 1 to 5% for Au^{-} , with Cs_2I^ {+} and Cs_3I _sp{2}{+} clusters as projectiles. Yields for the same surfaces using Cs ^{+} primary ions are much less than 1%, indicating that SI yields are enhanced with clusters. A yield enhancement occurs when the SI yield per atom of a polyatomic projectile is greater than the SI yield of its monoatomic equivalent, at the same velocity. Thus, a (M-H) ^{-} yield increase of a factor of 50, when phenylalanine is bombarded with Cs_3I_sp{2} {+} instead of Cs^{+ }, represents a yield enhancement factor of 10. For the projectiles and samples studied, it was observed that the heavier the mass of the constituents of a projectile, the larger the enhancement effects, and that the largest yield enhancements (with CsI and Au _ n projectiles) occur for the organic target, phenylalanine. One possible explanation for the larger enhancements with organics, namely a thermal spike process, appears unlikely. Experiments with high and low melting point isomers of dinitrostilbene, bombarded with Cs _2I^{+} and Cs^{+} projectiles, showed larger Cs_2I^ {+} yield enhancements for the high melting point isomer.
Silicon isotope ratio measurements by inductively coupled plasma tandem mass spectrometry for alteration studies of nuclear waste glasses.

PubMed

Gourgiotis, Alkiviadis; Ducasse, Thomas; Barker, Evelyne; Jollivet, Patrick; Gin, Stéphane; Bassot, Sylvain; Cazala, Charlotte

2017-02-15

High-level, long-lived nuclear waste arising from spent fuel reprocessing is vitrified in silicate glasses for final disposal in deep geologic formations. In order to better understand the mechanisms driving glass dissolution, glass alteration studies, based on silicon isotope ratio monitoring of 29 Si-doped aqueous solutions, were carried out in laboratories. This work explores the capabilities of the new type of quadrupole-based ICP-MS, the Agilent 8800 tandem quadrupole ICP-MS/MS, for accurate silicon isotope ratio determination for alteration studies of nuclear waste glasses. In order to avoid silicon polyatomic interferences, a new analytical method was developed using O 2 as the reaction gas in the Octopole Reaction System (ORS), and silicon isotopes were measured in mass-shift mode. A careful analysis of the potential polyatomic interferences on SiO + and SiO 2 + ion species was performed, and we found that SiO + ion species suffer from important polyatomic interferences coming from the matrix of sample and standard solutions (0.5M HNO 3 ). For SiO 2 + , no interferences were detected, and thus, these ion species were chosen for silicon isotope ratio determination. A number of key settings for accurate isotope ratio analysis like, detector dead time, integration time, number of sweeps, wait time offset, memory blank and instrumental mass fractionation, were considered and optimized. Particular attention was paid to the optimization of abundance sensitivity of the quadrupole mass filter before the ORS. We showed that poor abundance sensitivity leads to a significant shift of the data away from the Exponential Mass Fractionation Law (EMFL) due to the spectral overlaps of silicon isotopes combined with different oxygen isotopes (i.e. 28 Si 16 O 18 O + , 30 Si 16 O 16 O + ). The developed method was validated by measuring a series of reference solutions with different 29 Si enrichment. Isotope ratio trueness, uncertainty and repeatability were found to be <0.2%, <0.5% and <0.6%, respectively. These performances meet the requirements of the studies of nuclear glasses alteration and open up possibilities to use this method for precise determination of silicon content in natural samples by Isotope Dilution. Copyright © 2016 Elsevier B.V. All rights reserved.
LIMAO: Cross-platform software for simulating laser-induced alignment and orientation dynamics of linear-, symmetric- and asymmetric tops

NASA Astrophysics Data System (ADS)

Szidarovszky, Tamás; Jono, Maho; Yamanouchi, Kaoru

2018-07-01

A user-friendly and cross-platform software called Laser-Induced Molecular Alignment and Orientation simulator (LIMAO) has been developed. The program can be used to simulate within the rigid rotor approximation the rotational dynamics of gas phase molecules induced by linearly polarized intense laser fields at a given temperature. The software is implemented in the Java and Mathematica programming languages. The primary aim of LIMAO is to aid experimental scientists in predicting and analyzing experimental data representing laser-induced spatial alignment and orientation of molecules.
Theoretical investigation of gas-surface interactions

NASA Technical Reports Server (NTRS)

Dyall, Kenneth G.

1992-01-01

The investigation into the appearance of intruder states from the negative continuum when some of the two-electron integrals were omitted was completed. The work shows that, provided all integrals involving core contracted functions in an atomic general contraction are included, or that the core functions are radially localized, meaningful results are obtained and intruder states do not appear. In the area of program development, the Dirac-Hartree-Fock (DHF) program for closed-shell polyatomic molecules was extended to permit Kramers-restricted open-shell DHF calculations with one electron in an open shell or one hole in a closed shell, or state-averaged DHF calculations over several particle or hole doublet states. One application of the open-shell code was to the KO molecule. Another major area of program development is the transformation of integrals from the scalar basis in which they are generated to the 2-spinor basis employed in parts of the DHF program, and hence to supermatrix form. Particularly concerning the omission of small component integrals, and with increase in availability of disk space, it is now possible to consider transforming the integrals. The use of ordered integrals, either in the scalar basis or in the 2-spinor basis, would considerably speed up the construction of the Fock matrix, and even more so if supermatrices were constructed. A considerable amount of effort was spent on analyzing the integral ordering and tranformation for the DHF program. The work of assessing the reliability of the relativistic effective core potentials (RECPs) was continued with calculation of the group IV monoxides. The perturbation of the metal atom provided by oxygen is expected to be larger than that provided by hydrogen and thus provide a better test of the qualification of the RECPs. Calculations on some platinum hydrides were carried out at nonrelativistic (NR), perturbation theory (PT) and DHF levels. Reprints of four papers describing this work are included.
Predicting Bond Dissociation Energies of Transition-Metal Compounds by Multiconfiguration Pair-Density Functional Theory and Second-Order Perturbation Theory Based on Correlated Participating Orbitals and Separated Pairs.

PubMed

Bao, Junwei Lucas; Odoh, Samuel O; Gagliardi, Laura; Truhlar, Donald G

2017-02-14

We study the performance of multiconfiguration pair-density functional theory (MC-PDFT) and multireference perturbation theory for the computation of the bond dissociation energies in 12 transition-metal-containing diatomic molecules and three small transition-metal-containing polyatomic molecules and in two transition-metal dimers. The first step is a multiconfiguration self-consistent-field calculation, for which two choices must be made: (i) the active space and (ii) its partition into subspaces, if the generalized active space formulation is used. In the present work, the active space is chosen systematically by using three correlated-participating-orbitals (CPO) schemes, and the partition is chosen by using the separated-pair (SP) approximation. Our calculations show that MC-PDFT generally has similar accuracy to CASPT2, and the active-space dependence of MC-PDFT is not very great for transition-metal-ligand bond dissociation energies. We also find that the SP approximation works very well, and in particular SP with the fully translated BLYP functional SP-ftBLYP is more accurate than CASPT2. SP greatly reduces the number of configuration state functions relative to CASSCF. For the cases of FeO and NiO with extended-CPO active space, for which complete active space calculations are unaffordable, SP calculations are not only affordable but also of satisfactory accuracy. All of the MC-PDFT results are significantly better than the corresponding results with broken-symmetry spin-unrestricted Kohn-Sham density functional theory. Finally we test a perturbation theory method based on the SP reference and find that it performs slightly worse than CASPT2 calculations, and for most cases of the nominal-CPO active space, the approximate SP perturbation theory calculations are less accurate than the much less expensive SP-PDFT calculations.
Highly Accurate and Precise Infrared Transition Frequencies of the H_3^+ Cation

NASA Astrophysics Data System (ADS)

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 (<1 wn) corrections must be made to the to the traditional Born-Oppenheimer approximation that take into account not only adiabatic and non-adiabatic couplings, but quantum electrodynamic corrections as well. For the lowest rovibrational levels the agreement between theory and experiment is approaching 0.001 wn, whereas the agreement is on the order of 0.01 - 0.1 wn for higher levels which are closely rivaling the uncertainties on the experimental data. As method development for calculating these various corrections progresses it becomes necessary for the uncertainties on the experimental data to be improved in order to properly benchmark the calculations. Previously we have measured 20 rovibrational transitions of H_3^+ with MHz-level precision, all of which have arisen from low lying rotational levels. Here we present new measurements of rovibrational transitions arising from higher rotational and vibrational levels. These transitions not only allow for probing higher energies on the potential energy surface, but through the use of combination differences, will ultimately lead to prediction of the "forbidden" rotational transitions with MHz-level accuracy. L.G. 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.
Mitochondrial genome of the moon jelly Aurelia aurita (Cnidaria, Scyphozoa): A linear DNA molecule encoding a putative DNA-dependent DNA polymerase.

PubMed

Shao, Zhiyong; Graf, Shannon; Chaga, Oleg Y; Lavrov, Dennis V

2006-10-15

The 16,937-nuceotide sequence of the linear mitochondrial DNA (mt-DNA) molecule of the moon jelly Aurelia aurita (Cnidaria, Scyphozoa) - the first mtDNA sequence from the class Scypozoa and the first sequence of a linear mtDNA from Metazoa - has been determined. This sequence contains genes for 13 energy pathway proteins, small and large subunit rRNAs, and methionine and tryptophan tRNAs. In addition, two open reading frames of 324 and 969 base pairs in length have been found. The deduced amino-acid sequence of one of them, ORF969, displays extensive sequence similarity with the polymerase [but not the exonuclease] domain of family B DNA polymerases, and this ORF has been tentatively identified as dnab. This is the first report of dnab in animal mtDNA. The genes in A. aurita mtDNA are arranged in two clusters with opposite transcriptional polarities; transcription proceeding toward the ends of the molecule. The determined sequences at the ends of the molecule are nearly identical but inverted and lack any obvious potential secondary structures or telomere-like repeat elements. The acquisition of mitochondrial genomic data for the second class of Cnidaria allows us to reconstruct characteristic features of mitochondrial evolution in this animal phylum.
Differential solvation of intrinsically disordered linkers drives the formation of spatially organized droplets in ternary systems of linear multivalent proteins

NASA Astrophysics Data System (ADS)

Harmon, Tyler S.; Holehouse, Alex S.; Pappu, Rohit V.

2018-04-01

Intracellular biomolecular condensates are membraneless organelles that encompass large numbers of multivalent protein and nucleic acid molecules. The bodies assemble via a combination of liquid–liquid phase separation and gelation. A majority of condensates included multiple components and show multilayered organization as opposed to being well-mixed unitary liquids. Here, we put forward a simple thermodynamic framework to describe the emergence of spatially organized droplets in multicomponent systems comprising of linear multivalent polymers also known as associative polymers. These polymers, which mimic proteins and/or RNA have the architecture of domains or motifs known as stickers that are interspersed by flexible spacers known as linkers. Using a minimalist numerical model for a four-component system, we have identified features of linear multivalent molecules that are necessary and sufficient for generating spatially organized droplets. We show that differences in sequence-specific effective solvation volumes of disordered linkers between interaction domains enable the formation of spatially organized droplets. Molecules with linkers that are preferentially solvated are driven to the interface with the bulk solvent, whereas molecules that have linkers with negligible effective solvation volumes form cores in the core–shell architectures that emerge in the minimalist four-component systems. Our modeling has relevance for understanding the physical determinants of spatially organized membraneless organelles.
Research in Electronics - JSEP.

DTIC Science & Technology

1981-03-01

17. H . Helvajian and C. Wittig, "Collisional Quenching of HgBr(B 2 4i/2), Opt. Commun. 30, 189 (1979). 18. H . Reisler and C. Wittig, "Electronic...Luminescence Resulting from IR Multiple Photon Excitation, " in ’Photoselective Chemistry, Part I,’ J. Jortner ed., Wiley, 1981. 19. H . Helvajian , M...to Intramolecular V E coupling in IR Laser Excited Polyatomics, " J. Chem. Phys., in press. 22. H . Helvajian and C. Wittig, "Vibrational Quenching of
In Situ Determination of Trace Elements in Fish Otoliths by Laser Ablation Double Focusing Sector Field Inductively Coupled Plasma Mass Spectrometry Using a Solution Standard Addition Calibration Method

NASA Astrophysics Data System (ADS)

Chen, Z.; Jones, C. M.

2002-05-01

Microchemistry of fish otoliths (fish ear bones) is a very useful tool for monitoring aquatic environments and fish migration. However, determination of the elemental composition in fish otolith by ICP-MS has been limited to either analysis of dissolved sample solution or measurement of limited number of trace elements by laser ablation (LA)- ICP-MS due to low sensitivity, lack of available calibration standards, and complexity of polyatomic molecular interference. In this study, a method was developed for in situ determination of trace elements in fish otoliths by laser ablation double focusing sector field ultra high sensitivity Finnigan Element 2 ICP-MS using a solution standard addition calibration method. Due to the lack of matrix-match solid calibration standards, sixteen trace elements (Na, Mg, P, Cr, Mn, Fe, Ni, Cu, Rb, Sr, Y, Cd, La, Ba, Pb and U) were determined using a solution standard calibration with Ca as an internal standard. Flexibility, easy preparation and stable signals are the advantages of using solution calibration standards. In order to resolve polyatomic molecular interferences, medium resolution (M/delta M > 4000) was used for some elements (Na, Mg, P, Cr, Mn, Fe, Ni, and Cu). Both external calibration and standard addition quantification strategies are compared and discussed. Precision, accuracy, and limits of detection are presented.
Radiative interactions in molecular gases under local and nonlocal thermodynamic equilibrium conditions

NASA Technical Reports Server (NTRS)

Tiwari, S. N.; Jha, M. K.

1993-01-01

Basic formulations, analyses, and numerical procedures are presented to investigate radiative heat interactions in diatomic and polyatomic gases under local and nonlocal thermodynamic equilibrium conditions. Essential governing equations are presented for both gray and nongray gases. Information is provided on absorption models, relaxation times, and transfer equations. Radiative flux equations are developed which are applicable under local and nonlocal thermodynamic equilibrium conditions. The problem is solved for fully developed laminar incompressible flows between two parallel plates under the boundary condition of a uniform surface heat flux. For specific applications, three diatomic and three polyatomic gases are considered. The results are obtained numerically by employing the method of variation of parameters. The results are compared under local and nonlocal thermodynamic equilibrium conditions at different temperature and pressure conditions. Both gray and nongray studies are conducted extensively for all molecular gases considered. The particular gases selected for this investigation are CO, NO, OH, CO2, H2O, and CH4. The temperature and pressure range considered are 300-2000 K and 0.1-10 atmosphere, respectively. In general, results demonstrate that the gray gas approximation overestimates the effect of radiative interaction for all conditions. The conditions of NLTE, however, result in underestimation of radiative interactions. The method developed for this study can be extended to solve complex problems of radiative heat transfer involving nonequilibrium phenomena.
Ultracold Molecules in Optical Lattices: Efficient Production and Application to Molecular Clocks

DTIC Science & Technology

2015-05-03

near the intercombination- line threshold were measured for a variety of states, and explained by considering nonadiabatic effects ( Coriolis coupling) in...Moszynski, T. Zelevinsky. Nonadiabatic Effects in Ultracold Molecules via Anomalous Linear and Quadratic Zeeman Shifts, Physical Review Letters, (12...M. McDonald, G. Reinaudi, W. Skomorowski, R. Moszynski, T. Zelevinsky. Measurement of Nonadiabatic Effects in Ultracold Molecules via Anomalous
Field Effect Transistor in Nanoscale

DTIC Science & Technology

2017-04-26

analogues) and BxCyNz (Napathalene analogues with x+y+z=10) molecules using quantum many body approach coupled with kinetic (master) equations...analogues with x +y+z=10) molecules using quantum many body approach coupled with kinetic (master) equations. Interestingly, various types of non-linear...Small molecules (such as benzene), double quantum dots (like GaAs-based QDs) which are coupled weakly to metallic electrodes have shown their
Analysis of branched DNA replication and recombination intermediates from prokaryotic cells by two-dimensional (2D) native-native agarose gel electrophoresis.

PubMed

Robinson, Nicholas P

2013-01-01

Branched DNA molecules are generated by the essential processes of replication and recombination. Owing to their distinctive extended shapes, these intermediates migrate differently from linear double-stranded DNA under certain electrophoretic conditions. However, these branched species exist in the cell at much low abundance than the bulk linear DNA. Consequently, branched molecules cannot be visualized by conventional electrophoresis and ethidium bromide staining. Two-dimensional native-native agarose electrophoresis has therefore been developed as a method to facilitate the separation and visualization of branched replication and recombination intermediates. A wide variety of studies have employed this technique to examine branched molecules in eukaryotic, archaeal, and bacterial cells, providing valuable insights into how DNA is duplicated and repaired in all three domains of life.
Laser-induced emission spectroscopy of matrix-isolated carbon molecules: Experimental setup and new results on C3

NASA Astrophysics Data System (ADS)

Čermák, Ivo; Förderer, Markus; Čermáková, Iva; Kalhofer, Stefan; Stopka-Ebeler, Helmut; Monninger, Gerold; Krätschmer, Wolfgang

1998-06-01

We have studied small carbon molecules using a matrix-isolation technique. Our experimental setup is described in detail. The carbon clusters were produced by evaporating graphite and trapping the carbon-vapor molecules in solid argon, where molecular growth could be induced by controlled matrix annealing. To identify the produced molecules, absorption spectroscopy in the ultraviolet (UV)-visible and infrared (IR) spectral ranges was applied. Additional characterization of the excited and ground states of the molecules was obtained from emission and excitation spectra. The molecules were excited by a pulsed dye laser system and the emission spectra were recorded with a high-sensitivity photodiode-array spectrometer. We present our measurements on linear C3. The Ã 1Πu excited state of linear C3 was populated by the electronic transition Ã 1Πu←X˜ 1Σg+, and the corresponding excitation spectra of the C3 fluorescence (Ã 1Πu→X˜ 1Σg+) and phosphorescence (ã 3Πu→X˜ 1Σg+) were studied. Comparison of excitation and absorption spectra yielded information on site effects due to the matrix environment. Emission bands in the fluorescence and phosphorescence spectra up to vibrational energies of 8500 cm-1 could be observed. The radiation lifetime of the Ã 1Πu excited state of C3 in solid argon was found to be shorter than 10 ns. The phosphorescence transition ã 3Πu→X˜ 1Σg+ decays in about 10 ms and its rise indicates fast vibrational relaxation within the triplet system. Our data support a linear ground state geometry for C3 also in solid argon.

Crystal structure of cis-tetra-aqua-dichlorido-cobalt(II) sulfolane disolvate.

PubMed

Boudraa, Mhamed; Bouacida, Sofiane; Bouchareb, Hasna; Merazig, Hocine; Chtoun, El Hossain

2015-02-01

In the title compound, [CoCl2(H2O)4]·2C4H8SO2, the Co(II) cation is located on the twofold rotation axis and is coordinated by four water mol-ecules and two adjacent chloride ligands in a slightly distorted octa-hedral coordination environment. The cisoid angles are in the range 83.27 (5)-99.66 (2)°. The three transoid angles deviate significantly from the ideal linear angle. The crystal packing can be described as a linear arrangement of complex units along c formed by bifurcated O-H⋯Cl hydrogen bonds between two water mol-ecules from one complex unit towards one chloride ligand of the neighbouring complex. Two solvent mol-ecules per complex are attached to this infinite chain via O-H⋯O hydrogen bonds in which water mol-ecules act as the hydrogen-bond donor and sulfolane O atoms as the hydrogen-bond acceptor sites.
Measurement of a linear free energy relationship one molecule at a time

PubMed Central

Rao, B. V.; Kwon, K.-Y.; Liu, A.; Bartels, L.

2004-01-01

A systematic study of the dehydrogenation of substituted thiophenols by controlled charge injection from the tip of a scanning tunneling microscope (STM) reveals a pronounced dependence of the reaction yield on the position and the chemical nature of the substituent. We evaluate the dehydrogenation rate of para-halo-substituted species within a linear free energy relationship, namely the Hammett equation. The resultant ρ value of 1.4 can faithfully predict the reaction rates of molecules that are meta-halo-substituted or para-methyl-substituted. The positive sign of ρ suggests a negatively charged transition state at the core of the STM-induced process, and the magnitude of the ρ value indicates that the presence of the substrate does not preclude substantial substituent effects. The applicability of the Hammett equation to single-molecule chemistry offers facile prediction of the rate of STM-based single-molecule chemistry in a field, which so far has been addressed by focusing on involved quantum-mechanical modeling of its underlying processes. PMID:15601774
Measurement of a linear free energy relationship one molecule at a time.

PubMed

Rao, B V; Kwon, K-Y; Liu, A; Bartels, L

2004-12-28

A systematic study of the dehydrogenation of substituted thiophenols by controlled charge injection from the tip of a scanning tunneling microscope (STM) reveals a pronounced dependence of the reaction yield on the position and the chemical nature of the substituent. We evaluate the dehydrogenation rate of para-halo-substituted species within a linear free energy relationship, namely the Hammett equation. The resultant rho value of 1.4 can faithfully predict the reaction rates of molecules that are meta-halo-substituted or para-methyl-substituted. The positive sign of rho suggests a negatively charged transition state at the core of the STM-induced process, and the magnitude of the rho value indicates that the presence of the substrate does not preclude substantial substituent effects. The applicability of the Hammett equation to single-molecule chemistry offers facile prediction of the rate of STM-based single-molecule chemistry in a field, which so far has been addressed by focusing on involved quantum-mechanical modeling of its underlying processes.
How does the isomerization rate affect the photoisomerization-induced transport properties of a doped molecular glass-former?

NASA Astrophysics Data System (ADS)

Accary, J.-B.; Teboul, V.

2013-07-01

We investigate the effect of the isomerization rate f on the microscopic mechanisms at the origin of the massive mass transport found in glass-formers doped with isomerizing azobenzene molecules that result in surface relief gratings formation. To this end we simulate the isomerization of dispersed probe molecules embedded into a molecular host glass-former. The host diffusion coefficient first increases linearly with f and then saturates. The saturated value of the diffusion coefficient and of the viscosity does not depend on f but increases with temperature while the linear response for these transport coefficients depends only slightly on the temperature. We interpret this saturation as arising from the appearance of increasingly soft regions around the probes for high isomerization rates, a result in qualitative agreement with experiments. These two different physical behaviors, linear response and saturation, are reminiscent of the two different unexplained mass transport mechanisms observed for small or large light intensities (for small intensities the molecules move towards the dark regions while for large intensities they move towards the illuminated regions).
Scanning tunneling microscopy of the formation, transformation, and property of oligothiophene self-organizations on graphite and gold surfaces.

PubMed

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

2007-03-06

Two alkyl-substituted dual oligothiophenes, quarterthiophene (4T)-trimethylene (tm)-octithiophene (8T) and 4T-tm-4T, were used to fabricate molecular structures on highly oriented pyrolytic graphite and Au(111) surfaces. The resulted structures were investigated by scanning tunneling microscopy. The 4T-tm-8T and 4T-tm-4T molecules self-organize into long-range ordered structures with linear and/or quasi-hexagonal patterns on highly oriented pyrolytic graphite at ambient temperature. Thermal annealing induced a phase transformation from quasi-hexagonal to linear in 4T-tm-8T adlayer. The molecules adsorbed on Au(111) surface in randomly folded and linear conformation. Based on scanning tunneling microscopy results, the structural models for different self-organizations were proposed. Scanning tunneling spectroscopy measurement showed the electronic property of individual molecules in the patterns. These results are significant in understanding the chemistry of molecular structure, including its formation, transformation, and electronic properties. They also help to fabricate oligothiophene assemblies with desired structures for future molecular devices.
Structures, Bonding, and Energetics of Potential Triatomic Circumstellar Molecules Containing Group 15 and 16 Elements.

PubMed

Turner, Walter E; Agarwal, Jay; Schaefer, Henry F

2015-12-03

The recent discovery of PN in the oxygen-rich shell of the supergiant star VY Canis Majoris points to the formation of several triatomic molecules involving oxygen, nitrogen, and phosphorus; these are also intriguing targets for main-group synthetic inorganic chemistry. In this research, high-level ab initio electronic structure computations were conducted on the potential circumstellar molecule OPN and several of its heavier group 15 and 16 congeners (SPN, SePN, TePN, OPP, OPAs, and OPSb). For each congener, four isomers were examined. Optimized geometries were obtained with coupled cluster theory [CCSD(T)] using large Dunning basis sets [aug-cc-pVQZ, aug-cc-pV(Q+d)Z, and aug-cc-pVQZ-PP], and relative energies were determined at the complete basis set limit of CCSDT(Q) from focal point analyses. The linear phosphorus-centered molecules were consistently the lowest in energy of the group 15 congeners by at least 6 kcal mol(-1), resulting from double-triple and single-double bond resonances within the molecule. The linear nitrogen-centered molecules were consistently the lowest in energy of the group 16 congeners by at least 5 kcal mol(-1), due to the electronegative central nitrogen atom encouraging electron delocalization throughout the molecule. For OPN, OPP, and SPN, anharmonic vibrational frequencies and vibrationally corrected rotational constants are predicted; good agreement with available experimental data is observed.
DNA confinement in nanochannels: physics and biological applications

NASA Astrophysics Data System (ADS)

Reisner, Walter; Pedersen, Jonas N.; Austin, Robert H.

2012-10-01

DNA is the central storage molecule of genetic information in the cell, and reading that information is a central problem in biology. While sequencing technology has made enormous advances over the past decade, there is growing interest in platforms that can readout genetic information directly from long single DNA molecules, with the ultimate goal of single-cell, single-genome analysis. Such a capability would obviate the need for ensemble averaging over heterogeneous cellular populations and eliminate uncertainties introduced by cloning and molecular amplification steps (thus enabling direct assessment of the genome in its native state). In this review, we will discuss how the information contained in genomic-length single DNA molecules can be accessed via physical confinement in nanochannels. Due to self-avoidance interactions, DNA molecules will stretch out when confined in nanochannels, creating a linear unscrolling of the genome along the channel for analysis. We will first review the fundamental physics of DNA nanochannel confinement—including the effect of varying ionic strength—and then discuss recent applications of these systems to genomic mapping. Apart from the intense biological interest in extracting linear sequence information from elongated DNA molecules, from a physics view these systems are fascinating as they enable probing of single-molecule conformation in environments with dimensions that intersect key physical length-scales in the 1 nm to 100 µm range.
DNA confinement in nanochannels: physics and biological applications.

PubMed

Reisner, Walter; Pedersen, Jonas N; Austin, Robert H

2012-10-01

DNA is the central storage molecule of genetic information in the cell, and reading that information is a central problem in biology. While sequencing technology has made enormous advances over the past decade, there is growing interest in platforms that can readout genetic information directly from long single DNA molecules, with the ultimate goal of single-cell, single-genome analysis. Such a capability would obviate the need for ensemble averaging over heterogeneous cellular populations and eliminate uncertainties introduced by cloning and molecular amplification steps (thus enabling direct assessment of the genome in its native state). In this review, we will discuss how the information contained in genomic-length single DNA molecules can be accessed via physical confinement in nanochannels. Due to self-avoidance interactions, DNA molecules will stretch out when confined in nanochannels, creating a linear unscrolling of the genome along the channel for analysis. We will first review the fundamental physics of DNA nanochannel confinement--including the effect of varying ionic strength--and then discuss recent applications of these systems to genomic mapping. Apart from the intense biological interest in extracting linear sequence information from elongated DNA molecules, from a physics view these systems are fascinating as they enable probing of single-molecule conformation in environments with dimensions that intersect key physical length-scales in the 1 nm to 100 µm range.
Quantum coherent π-electron rotations in a non-planar chiral molecule induced by using a linearly polarized UV laser pulse

NASA Astrophysics Data System (ADS)

Mineo, Hirobumi; Fujimura, Yuichi

2015-06-01

We propose an ultrafast quantum switching method of π-electron rotations, which are switched among four rotational patterns in a nonplanar chiral aromatic molecule (P)-2,2’- biphenol and perform the sequential switching among four rotational patterns which are performed by the overlapped pump-dump laser pulses. Coherent π-electron dynamics are generated by applying the linearly polarized UV pulse laser to create a pair of coherent quasidegenerated excited states. We also plot the time-dependent π-electron ring current, and discussed ring current transfer between two aromatic rings.
Relativistic properties of a molecule: energy, linear momentum, angular momentum and boost momentum to order 1/c 2

NASA Astrophysics Data System (ADS)

Cameron, Robert P.; Cotter, J. P.

2018-05-01

We give an explicit and general description of the energy, linear momentum, angular momentum and boost momentum of a molecule to order 1/c 2, where it necessary to take account of kinetic contributions made by the electrons and nuclei as well as electromagnetic contributions made by the intramolecular field. A wealth of interesting subtleties are encountered that are not seen at order 1/c 0, including relativistic Hall shifts, anomalous velocities and hidden momenta. Some of these have well known analogues in solid state physics.
Dynamic fluctuations in single-molecule biophysics experiments. Comment on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb and S.K. Sarkar

NASA Astrophysics Data System (ADS)

Krapf, Diego

2015-06-01

Single-molecule biophysics includes the study of isolated molecules and that of individual molecules within living cells. In both cases, dynamic fluctuations at the nanoscale play a critical role. Colomb and Sarkar emphasize how different noise sources affect the analysis of single molecule data [1]. Fluctuations in biomolecular systems arise from two very different mechanisms. On one hand thermal fluctuations are a predominant feature in the behavior of individual molecules. On the other hand, non-Gaussian fluctuations can arise from inter- and intramolecular interactions [2], spatial heterogeneities [3], non-Poisson external perturbations [4] and complex non-linear dynamics in general [5,6].
Mechanical response of collagen molecule under hydrostatic compression.

PubMed

Saini, Karanvir; Kumar, Navin

2015-04-01

Proteins like collagen are the basic building blocks of various body tissues (soft and hard). Collagen molecules find their presence in the skeletal system of the body where they bear mechanical loads from different directions, either individually or along with hydroxy-apatite crystals. Therefore, it is very important to understand the mechanical behavior of the collagen molecule which is subjected to multi-axial state of loading. The estimation of strains of collagen molecule along different directions resulting from the changes in hydrostatic pressure magnitude, can provide us new insights into its mechanical behavior. In the present work, full atomistic simulations have been used to study global (volumetric) as well as local (along different directions) mechanical properties of the hydrated collagen molecule which is subjected to different hydrostatic pressure magnitudes. To estimate the local mechanical properties, the strains of collagen molecule along its longitudinal and transverse directions have been acquired at different hydrostatic pressure magnitudes. In spite of non-homogeneous distribution of atoms within the collagen molecule, the calculated values of local mechanical properties have been found to carry the same order of magnitude along the longitudinal and transverse directions. It has been demonstrated that the values of global mechanical properties like compressibility, bulk modulus, etc. as well as local mechanical properties like linear compressibility, linear elastic modulus, etc. are functions of magnitudes of applied hydrostatic pressures. The mechanical characteristics of collagen molecule based on the atomistic model have also been compared with that of the continuum model in the present work. The comparison showed up orthotropic material behavior for the collagen molecule. The information on collagen molecule provided in the present study can be very helpful in designing the future bio-materials. Copyright © 2015 Elsevier B.V. All rights reserved.
Derivation of a formula for the resonance integral for a nonorthogonal basis set

PubMed Central

Yim, Yung-Chang; Eyring, Henry

1981-01-01

In a self-consistent field calculation, a formula for the off-diagonal matrix elements of the core Hamiltonian is derived for a nonorthogonal basis set by a polyatomic approach. A set of parameters is then introduced for the repulsion integral formula of Mataga-Nishimoto to fit the experimental data. The matrix elements computed for the nonorthogonal basis set in the π-electron approximation are transformed to those for an orthogonal basis set by the Löwdin symmetrical orthogonalization. PMID:16593009
Adiabatic Field-Free Alignment of Asymmetric Top Molecules with an Optical Centrifuge.

PubMed

Korobenko, A; Milner, V

2016-05-06

We use an optical centrifuge to align asymmetric top SO_{2} molecules by adiabatically spinning their most polarizable O-O axis. The effective centrifugal potential in the rotating frame confines the sulfur atoms to the plane of the laser-induced rotation, leading to the planar molecular alignment that persists after the molecules are released from the centrifuge. The periodic appearance of the full three-dimensional alignment, typically observed only with linear and symmetric top molecules, is also detected. Together with strong in-plane centrifugal forces, which bend the molecules by up to 10 deg, permanent field-free alignment offers new ways of controlling molecules with laser light.
Molecular structure, supramolecular organization and thermotropic phase behavior of N-acylglycine alkyl esters with matched acyl and alkyl chains.

PubMed

Reddy, S Thirupathi; Swamy, Musti J

2017-11-01

N-Acylglycines (NAGs), the endogenous single-tailed lipids present in rat brain and other mammalian tissues, play significant roles in cell physiology and exhibit interesting pharmacological properties. In the present study, a homologous series of N-acylglycine alkyl esters (NAGEs) with matched chains were synthesized and characterized. Results of differential scanning calorimetric studies revealed that all NAGEs exhibit a single sharp phase transition and that the transition enthalpy and entropy show a linear dependence on the N-acyl and ester alkyl chain length. The structure of N-myristoylglycine myristyl ester (NMGME), solved by single-crystal X-ray diffraction, showed that the molecule adopts a linear geometry and revealed that the structure of N-myristoyl glycyl moiety in NMGME is identical to that in N-myristoylglycine. The molecules are packed in layers with the polar functional groups of the ester and amide functionalities located at the center of the layer. The crystal packing is stabilized by NH⋯O hydrogen bonds between the amide CO and NH groups of adjacent molecules as well as by CH⋯O hydrogen bonds between the amide carbonyl and the methylene CH adjacent to the ester carbonyl of neighboring molecules as well as between ester carbonyl and methylene group of the glycine moiety of adjacent molecules. Powder X-ray diffraction studies showed a linear dependence of the d-spacings on the acyl chain length, suggesting that all NAGEs adopt a structure similar to the packing exhibited in the crystal lattice of NMGME. Copyright © 2017 Elsevier B.V. All rights reserved.
Third-order-harmonic generation in coherently spinning molecules

NASA Astrophysics Data System (ADS)

Prost, E.; Zhang, H.; Hertz, E.; Billard, F.; Lavorel, B.; Bejot, P.; Zyss, Joseph; Averbukh, Ilya Sh.; Faucher, O.

2017-10-01

The rotational Doppler effect occurs when circularly polarized light interacts with a rotating anisotropic material. It is manifested by the appearance of a spectral shift ensuing from the transfer of angular momentum and energy between radiation and matter. Recently, we reported terahertz-range rotational Doppler shifts produced in third-order nonlinear optical conversion [O. Faucher et al., Phys. Rev. A 94, 051402(R) (2016), 10.1103/PhysRevA.94.051402]. The experiment was performed in an ensemble of coherently spinning molecules prepared by a short laser pulse exhibiting a twisted linear polarization. The present work provides an extensive analysis of the rotational Doppler effect in third-order-harmonic generation from spinning linear molecules. The underlying physics is investigated both experimentally and theoretically. The implication of the rotational Doppler effect in higher-order processes like high-order-harmonic generation is discussed.
Organic molecules, ions, and rare isotopologues in the remnant of the stellar-merger candidate, CK Vulpeculae (Nova 1670)

NASA Astrophysics Data System (ADS)

Kamiński, T.; Menten, K. M.; Tylenda, R.; Karakas, A.; Belloche, A.; Patel, N. A.

2017-11-01

Context. CK Vulpeculae (CK Vul) is an enigmatic star whose outburst was observed in 1670-72. A stellar-merger event was proposed to explain its ancient eruption. Aims: We aim to investigate the composition of the molecular gas recently discovered in the remnant of CK Vul. Deriving the chemical, elemental, and isotopic composition is crucial for identifying the nature of the object and obtaining clues on its progenitor(s). Methods: We observed millimeter and submillimeter-wave spectra of CK Vul using the IRAM 30 m and APEX telescopes. Radiative-transfer modeling of the observed molecular features was performed to yield isotopic ratios for various elements. Results: The spectra of CK Vul reveal a very rich molecular environment of low excitation (Tex ≲ 12 K). Atomic carbon and twenty-seven different molecules, including two ions, were identified. They range from simple diatomic to complex polyatomic species of up to seven atoms large. The chemical composition of the molecular gas is indicative of carbon and nitrogen-driven chemistry but oxides are also present. Additionally, the abundance of fluorine may be enhanced. The spectra are rich in isotopologues that are very rare in most known sources. All stable isotopes of C, N, O, Si, and S are observed and their isotopic ratios are derived. Conclusions: The composition of the remnant's molecular gas is most peculiar and gives rise to a very unique millimeter and submillimeter spectrum. The observation of ions and complex molecules suggests the presence of a photoionizing source but its nature (a central star or shocks) remains unknown. The elemental and isotopic composition of the gas cannot be easily reconciled with standard stellar nucleosynthesis but processing in hot CNO cycles and partial helium burning can explain most of the chemical peculiarities. The isotopic ratios of CK Vul are remarkably close to those of presolar "nova grains" but the link of Nova 1670 to objects responsible for these grains is unclear. The accuracy of isotopic ratios can be improved by future observations at higher angular resolutions and with realistic models of the kinematical structure of the remnant. The reduced spectra are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/607/A78
The Ionic Building Blocks of Life: Exploring Astrochemistry through Mass Spectrometry

NASA Astrophysics Data System (ADS)

Cole, Callie A.

The first polyatomic molecule was discovered in interstellar space in 1968, catalyzing the growth of a new scientific field called astrochemistry. Since its inception, collaborations among laboratory chemists, astrophysical modelers, and observational astronomers in this field have led to the detection of nearly 200 molecules in the interstellar medium (ISM). Similarly, detections of complex biomolecules in cometary dust and meteorites have sparked theories of the origin of terrestrial life, a central focus of the recently-established field of astrobiology. Chemical processing occurs in a variety of environments within our galaxy. The purpose of this work is to explore the chemistry of ions and molecules that are pertinent to a multitude of these regions including nebulae, prestellar cores, and the atmosphere of Saturn's moon, Titan. This thesis presents mass spectrometric investigations of gas-phase ion chemistry that contribute to the fields of both astrochemistry and astrobiology. Many gas-phase chemical reactions are initiated by ions due to the attractive forces induced by their charge on a reacting partner. This attraction often lowers the barriers of ion-neutral reactions, and can lead to high reaction rates even at low temperatures. The ions examined herein increase in complexity starting with simple species (CN-) and concluding with larger biomolecules, the deprotonated nucleobases. This work begins with a series of Flowing Afterglow-Selected Ion Flow Tube (FA-SIFT) experiments exploring nitrogen-containing carbanion (C xNy-) chemistry and the formation of interstellar propene and methyl formate (Chapters 3 and 4). Reactions between CxN y- and H atoms reveal pathways for destruction of several CxN- and CxN2 - anions, but no reactions are observed for CxN3 - species. Two previously-proposed reactions between organic cations and H2 are shown to be immeasurably slow and unlikely to produce propene. Lastly, a reaction pathway producing protonated trans-methyl formate is experimentally and computationally verified. The later chapters describe studies of heterocyclic biomolecules performed using a modified ion trap apparatus. These ions include deprotonated azoles, pyrimidines, and purines (Chapters 5-7). In addition to their reactivity, the dissociation processes and fragments of these anions provide clues to potential precursors and abiotic syntheses. Notably, nearly all fragments observed are detected interstellar species.
Nanopores and nucleic acids: prospects for ultrarapid sequencing

NASA Technical Reports Server (NTRS)

Deamer, D. W.; Akeson, M.

2000-01-01

DNA and RNA molecules can be detected as they are driven through a nanopore by an applied electric field at rates ranging from several hundred microseconds to a few milliseconds per molecule. The nanopore can rapidly discriminate between pyrimidine and purine segments along a single-stranded nucleic acid molecule. Nanopore detection and characterization of single molecules represents a new method for directly reading information encoded in linear polymers. If single-nucleotide resolution can be achieved, it is possible that nucleic acid sequences can be determined at rates exceeding a thousand bases per second.
Recycling of protein subunits during DNA translocation and cleavage by Type I restriction-modification enzymes

PubMed Central

Simons, Michelle; Szczelkun, Mark D.

2011-01-01

The Type I restriction-modification enzymes comprise three protein subunits; HsdS and HsdM that form a methyltransferase (MTase) and HsdR that associates with the MTase and catalyses Adenosine-5′-triphosphate (ATP)-dependent DNA translocation and cleavage. Here, we examine whether the MTase and HsdR components can ‘turnover’ in vitro, i.e. whether they can catalyse translocation and cleavage events on one DNA molecule, dissociate and then re-bind a second DNA molecule. Translocation termination by both EcoKI and EcoR124I leads to HsdR dissociation from linear DNA but not from circular DNA. Following DNA cleavage, the HsdR subunits appear unable to dissociate even though the DNA is linear, suggesting a tight interaction with the cleaved product. The MTases of EcoKI and EcoAI can dissociate from DNA following either translocation or cleavage and can initiate reactions on new DNA molecules as long as free HsdR molecules are available. In contrast, the MTase of EcoR124I does not turnover and additional cleavage of circular DNA is not observed by inclusion of RecBCD, a helicase–nuclease that degrades the linear DNA product resulting from Type I cleavage. Roles for Type I restriction endonuclease subunit dynamics in restriction alleviation in the cell are discussed. PMID:21712244

TRES survey of variable diffuse interstellar bands

NASA Astrophysics Data System (ADS)

Law, Charles J.; Milisavljevic, Dan; Crabtree, Kyle N.; Johansen, Sommer L.; Patnaude, Daniel J.; Margutti, Raffaella; Parrent, Jerod T.; Drout, Maria R.; Sanders, Nathan E.; Kirshner, Robert P.; Latham, David W.

2017-09-01

Diffuse interstellar bands (DIBs) are absorption features commonly observed in optical/near-infrared spectra of stars and thought to be associated with polyatomic molecules that comprise a significant reservoir of organic material in the Universe. However, the central wavelengths of almost all DIBs do not correspond with electronic transitions of known atomic or molecular species and the specific physical nature of their carriers remains inconclusive despite decades of observational, theoretical and experimental research. It is well established that DIB carriers are located in the interstellar medium, but the recent discovery of time-varying DIBs in the spectra of the extragalactic supernova SN 2012ap suggests that some may be created in massive star environments. Here, we report evidence of short time-scale (∼10-60 d) changes in DIB absorption line substructure towards 3 of 17 massive stars observed as part of a pathfinder survey of variable DIBs conducted with the 1.5-m Tillinghast telescope and Tillinghast Reflector Echelle Spectrograph (TRES) at Fred L. Whipple Observatory. The detections are made in high-resolution optical spectra (R ∼ 44 000) having signal-to-noise ratios of 5-15 around the 5797 and 6614 Å features, and are considered significant but requiring further investigation. We find that these changes are potentially consistent with interactions between stellar winds and DIB carriers in close proximity. Our findings motivate a larger survey to further characterize these variations and may establish a powerful new method for probing the poorly understood physical characteristics of DIB carriers.
TRES Survey of Variable Diffuse Interstellar Bands

NASA Astrophysics Data System (ADS)

Law, Charles; Milisavljevic, Dan; Crabtree, Kyle; Johansen, Sommer; Patnaude, Daniel

2017-01-01

Diffuse interstellar bands (DIBs) are absorption features commonly observed in optical/near-infrared spectra of stars and thought to be associated with polyatomic molecules that comprise a significant reservoir of organic material in the universe. However, because the central wavelengths of DIBs do not correspond with electronic transitions of known atomic or molecular species, the specific physical nature of their carriers remains inconclusive despite decades of observational, theoretical, and experimental research. It is well established that DIB carriers must be located in the interstellar medium, but the recent discovery of time-varying DIBs in the spectra of the extragalactic supernova SN 2012ap suggests that some may be created in massive star environments. We report evidence of short time-scale (˜1-60 days) variations in DIB absorption line substructure toward 3 of 17 massive stars observed as part of a pathfinder survey of variable DIBs. The detections are made in high-resolution optical spectra (R ˜ 44000) from the Tillinghast Reflection Echelle Spectrograph on the 1.5m Tillinghast telescope at the Smithsonian Astrophysical Observatory's Fred L. Whipple Observatory on Mt. Hopkins in Arizona. Our detections have signal-to-noise ratios of 5-15 around the features of interest, and are thus considered significant but requiring further investigation. We find that these changes are potentially consistent with interactions between stellar winds and DIB carriers in close proximity. Our findings motivate a larger survey to further characterize these variations and may establish a powerful new method for probing the poorly understood physical characteristics of DIB carriers.
Mutual diffusion coefficients of heptane isomers in nitrogen: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Chae, Kyungchan; Violi, Angela

2011-01-01

The accurate knowledge of transport properties of pure and mixture fluids is essential for the design of various chemical and mechanical systems that include fluxes of mass, momentum, and energy. In this study we determine the mutual diffusion coefficients of mixtures composed of heptane isomers and nitrogen using molecular dynamics (MD) simulations with fully atomistic intermolecular potential parameters, in conjunction with the Green-Kubo formula. The computed results were compared with the values obtained using the Chapman-Enskog (C-E) equation with Lennard-Jones (LJ) potential parameters derived from the correlations of state values: MD simulations predict a maximum difference of 6% among isomers while the C-E equation presents that of 3% in the mutual diffusion coefficients in the temperature range 500-1000 K. The comparison of two approaches implies that the corresponding state principle can be applied to the models, which are only weakly affected by the anisotropy of the interaction potentials and the large uncertainty will be included in its application for complex polyatomic molecules. The MD simulations successfully address the pure effects of molecular structure among isomers on mutual diffusion coefficients by revealing that the differences of the total mutual diffusion coefficients for the six mixtures are caused mainly by heptane isomers. The cross interaction potential parameters, collision diameter σ _{12}, and potential energy well depth \\varepsilon _{12} of heptane isomers and nitrogen mixtures were also computed from the mutual diffusion coefficients.
Mass spectral analysis and imaging of tissue by ToF-SIMS--The role of buckminsterfullerene, C60+, primary ions

NASA Astrophysics Data System (ADS)

Jones, Emrys A.; Lockyer, Nicholas P.; Vickerman, John C.

2007-02-01

Recent developments in desorption/ionisation mass spectrometry techniques have made their application to biological analysis a realistic and successful proposition. Developments in primary ion source technology, mainly through the advent of polyatomic ion beams, have meant that the technique of secondary ion mass spectrometry (SIMS) can now access the depths of information required to allow biological imaging to be a viable option. Here the role of the primary ion C60+ is assessed with regard to molecular imaging of lipids and pharmaceuticals within tissue sections. High secondary ion yields and low surface damage accumulation are demonstrated on both model and real biological samples, indicating the high secondary ion efficiency afforded to the analyst by this primary ion when compared to other cluster ion beams used in imaging. The newly developed 40 keV C60+ ion source allows the beam to be focused such that high resolution imaging is demonstrated on a tissue sample, and the greater yields allow the molecular signal from the drug raclopride to be imaged within tissue section following in vivo dosing. The localisation shown for this drug alludes to issues regarding the chemical environment affecting the ionisation probability of the molecule; the importance of this effect is demonstrated with model systems and the possibility of using laser post-ionisation as a method for reducing this consequence of bio-sample complexity is demonstrated and discussed.
The gas phase structure of transition metal dihydrides

NASA Astrophysics Data System (ADS)

Demuynck, Jean; Schaefer, Henry F.

1980-01-01

ESR and infrared spectroscopic measurements on matrix isolated MnH2 and CrH2 have recently suggested that these simple molecules may be bent. This result would be the opposite of that found experimentally for the transition metal dihalides MX2, known to be linear. Here the geometrical structure of MnH2 has been investigated by molecular electronic structure theory. A large contracted Gaussian basis set [Mn(14s11p6p/9s8p3d), H(5s1p/3s1p)] was used in conjunction with self-consistent field and configuration interaction methods. These suggest that the 6A1 ground state of MnH2 is linear. Further studies of the 3A1 state (one of several low-lying states) of TiH2 also favor linearity, although this potential energy surface is extremely flat with respect to bending. Thus it appears probable that most MH2 molecules, like the related MX2 family, are linear.
Structural and vibrational characteristics of a non-linear optical material 3-(4-nitrophenyl)-1-(pyridine-3-yl) prop-2-en-1-one probed by quantum chemical computation and spectroscopic techniques

NASA Astrophysics Data System (ADS)

Kumar, Ram; Karthick, T.; Tandon, Poonam; Agarwal, Parag; Menezes, Anthoni Praveen; Jayarama, A.

2018-07-01

Chalcone and its derivatives are well-known for their high non-linear optical behavior and charge transfer characteristics. The effectiveness of charge transfer via ethylenic group and increase in NLO response of the chalcone upon substitutions are of great interest. The present study focuses the structural, charge transfer and non-linear optical properties of a new chalcone derivative "3-(4-nitrophenyl)-1-(pyridine-3-yl) prop-2-en-1-one" (hereafter abbreviated as 4 NP3AP). To accomplish this task, we have incorporated the experimental FT-IR, FT-Raman and UV-vis spectroscopic studies along with quantum chemical calculations. The frequency assignments of peaks in IR and Raman have been done on the basis of potential energy distribution and the results were compared with the earlier reports on similar kind of molecules. For obtaining the electronic transition details of 4 NP3AP, UV-vis spectrum has been simulated by considering both gaseous and solvent phase using time-dependent density functional theory (TD-DFT). The HOMO-LUMO energy gap, most important factor to be considered for studying charge transfer properties of the molecule has been calculated. The electron density surface map corresponding to the net electrostatic point charges has been generated to obtain the electrophilic and nucleophilic sites. The charge transfer originating from the occupied (donor) and unoccupied (acceptor) molecular orbitals have been analyzed with the help of natural bond orbital theory. Moreover, the estimation of second-hyperpolarizability of the molecule confirms the non-linear optical behavior of the molecule.
Model of DNA topology simplification has come full (supercoiled) circle after two decades of research. Comment on "Disentangling DNA molecules" by Alexander Vologodskii

NASA Astrophysics Data System (ADS)

Stasiak, Andrzej

2016-09-01

Being a geek of DNA topology, I remember very well the stir caused by 1997 Science paper showing that DNA topoisomerases have the ability to simplify DNA topology below the topological equilibrium values [1]. In their seminal experiments Rybenkov et al. [1] started with linear double-stranded DNA molecules with cohesive ends. The mutual cohesiveness of DNA ends was due to mutual complementarity of single-stranded extensions at both ends of linear double-stranded DNA molecules. When such DNA molecules were heated up and then slowly cooled down the single-stranded ends eventually annealed with each other causing DNA circularization. This experimental protocol permitted the authors to establish topological/thermodynamic equilibrium within samples of circularized DNA molecules. Among simple unknotted circles one also observed knotted and catenated DNA molecules. The fraction of knotted molecules in DNA samples at topological equilibrium was increasing with the length of DNA molecules undergoing slow circularization. The fraction of catenated molecules was increasing with the length and the concentration of the molecules undergoing slow circularization. Rybenkov et al. incubated then such equilibrated DNA samples with type II DNA topoisomerases, which pass DNA duplex regions through each other, and observed that as the result of it the fraction of knotted and catenated DNA molecules was dramatically decreased (up to 80-fold). This elegant experiment indicated for the first time that type II DNA topoisomerases acting on knotted or catenated DNA molecules have the ability to select among many potential sites of DNA-DNA passages these that result in DNA unknotting or decatenation. Without such a selection topoisomerases could only maintain the original topological equilibrium obtained during the slow cyclization. The big question was how DNA topoisomerases can be directed to do DNA-DNA passages that preferentially result in DNA unknotting and decatenation.
High-harmonic spectroscopy of aligned molecules

NASA Astrophysics Data System (ADS)

Yun, Hyeok; Yun, Sang Jae; Lee, Gae Hwang; Nam, Chang Hee

2017-01-01

High harmonics emitted from aligned molecules driven by intense femtosecond laser pulses provide the opportunity to explore the structural information of molecules. The field-free molecular alignment technique is an expedient tool for investigating the structural characteristics of linear molecules. The underlying physics of field-free alignment, showing the characteristic revival structure specific to molecular species, is clearly explained from the quantum-phase analysis of molecular rotational states. The anisotropic nature of molecules is shown from the harmonic polarization measurement performed with spatial interferometry. The multi-orbital characteristics of molecules are investigated using high-harmonic spectroscopy, applied to molecules of N2 and CO2. In the latter case the two-dimensional high-harmonic spectroscopy, implemented using a two-color laser field, is applied to distinguish harmonics from different orbitals. Molecular high-harmonic spectroscopy will open a new route to investigate ultrafast dynamics of molecules.
Length-dependent thermal transport in one-dimensional self-assembly of planar π-conjugated molecules

NASA Astrophysics Data System (ADS)

Tang, Hao; Xiong, Yucheng; Zu, Fengshuo; Zhao, Yang; Wang, Xiaomeng; Fu, Qiang; Jie, Jiansheng; Yang, Juekuan; Xu, Dongyan

2016-06-01

This work reports a thermal transport study in quasi-one-dimensional organic nanostructures self-assembled from conjugated planar molecules via π-π interactions. Thermal resistances of single crystalline copper phthalocyanine (CuPc) and perylenetetracarboxylic diimide (PTCDI) nanoribbons are measured via a suspended thermal bridge method. We experimentally observed the deviation from the linear length dependence for the thermal resistance of single crystalline β-phase CuPc nanoribbons, indicating possible subdiffusion thermal transport. Interestingly, a gradual transition to the linear length dependence is observed with the increase of the lateral dimensions of CuPc nanoribbons. The measured thermal resistance of single crystalline CuPc nanoribbons shows an increasing trend with temperature. However, the trend of temperature dependence of thermal resistance is reversed after electron irradiation, i.e., decreasing with temperature, indicating that the single crystalline CuPc nanoribbons become `amorphous'. Similar behavior is also observed for PTCDI nanoribbons after electron irradiation, proving that the electron beam can induce amorphization of single crystalline self-assembled nanostructures of planar π-conjugated molecules. The measured thermal resistance of the `amorphous' CuPc nanoribbon demonstrates a roughly linear dependence on the nanoribbon length, suggesting that normal diffusion dominates thermal transport.This work reports a thermal transport study in quasi-one-dimensional organic nanostructures self-assembled from conjugated planar molecules via π-π interactions. Thermal resistances of single crystalline copper phthalocyanine (CuPc) and perylenetetracarboxylic diimide (PTCDI) nanoribbons are measured via a suspended thermal bridge method. We experimentally observed the deviation from the linear length dependence for the thermal resistance of single crystalline β-phase CuPc nanoribbons, indicating possible subdiffusion thermal transport. Interestingly, a gradual transition to the linear length dependence is observed with the increase of the lateral dimensions of CuPc nanoribbons. The measured thermal resistance of single crystalline CuPc nanoribbons shows an increasing trend with temperature. However, the trend of temperature dependence of thermal resistance is reversed after electron irradiation, i.e., decreasing with temperature, indicating that the single crystalline CuPc nanoribbons become `amorphous'. Similar behavior is also observed for PTCDI nanoribbons after electron irradiation, proving that the electron beam can induce amorphization of single crystalline self-assembled nanostructures of planar π-conjugated molecules. The measured thermal resistance of the `amorphous' CuPc nanoribbon demonstrates a roughly linear dependence on the nanoribbon length, suggesting that normal diffusion dominates thermal transport. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr09043a
Many-Body Descriptors for Predicting Molecular Properties with Machine Learning: Analysis of Pairwise and Three-Body Interactions in Molecules.

PubMed

Pronobis, Wiktor; Tkatchenko, Alexandre; Müller, Klaus-Robert

2018-06-12

Machine learning (ML) based prediction of molecular properties across chemical compound space is an important and alternative approach to efficiently estimate the solutions of highly complex many-electron problems in chemistry and physics. Statistical methods represent molecules as descriptors that should encode molecular symmetries and interactions between atoms. Many such descriptors have been proposed; all of them have advantages and limitations. Here, we propose a set of general two-body and three-body interaction descriptors which are invariant to translation, rotation, and atomic indexing. By adapting the successfully used kernel ridge regression methods of machine learning, we evaluate our descriptors on predicting several properties of small organic molecules calculated using density-functional theory. We use two data sets. The GDB-7 set contains 6868 molecules with up to 7 heavy atoms of type CNO. The GDB-9 set is composed of 131722 molecules with up to 9 heavy atoms containing CNO. When trained on 5000 random molecules, our best model achieves an accuracy of 0.8 kcal/mol (on the remaining 1868 molecules of GDB-7) and 1.5 kcal/mol (on the remaining 126722 molecules of GDB-9) respectively. Applying a linear regression model on our novel many-body descriptors performs almost equal to a nonlinear kernelized model. Linear models are readily interpretable: a feature importance ranking measure helps to obtain qualitative and quantitative insights on the importance of two- and three-body molecular interactions for predicting molecular properties computed with quantum-mechanical methods.
Detection of kinetic change points in piece-wise linear single molecule motion

NASA Astrophysics Data System (ADS)

Hill, Flynn R.; van Oijen, Antoine M.; Duderstadt, Karl E.

2018-03-01

Single-molecule approaches present a powerful way to obtain detailed kinetic information at the molecular level. However, the identification of small rate changes is often hindered by the considerable noise present in such single-molecule kinetic data. We present a general method to detect such kinetic change points in trajectories of motion of processive single molecules having Gaussian noise, with a minimum number of parameters and without the need of an assumed kinetic model beyond piece-wise linearity of motion. Kinetic change points are detected using a likelihood ratio test in which the probability of no change is compared to the probability of a change occurring, given the experimental noise. A predetermined confidence interval minimizes the occurrence of false detections. Applying the method recursively to all sub-regions of a single molecule trajectory ensures that all kinetic change points are located. The algorithm presented allows rigorous and quantitative determination of kinetic change points in noisy single molecule observations without the need for filtering or binning, which reduce temporal resolution and obscure dynamics. The statistical framework for the approach and implementation details are discussed. The detection power of the algorithm is assessed using simulations with both single kinetic changes and multiple kinetic changes that typically arise in observations of single-molecule DNA-replication reactions. Implementations of the algorithm are provided in ImageJ plugin format written in Java and in the Julia language for numeric computing, with accompanying Jupyter Notebooks to allow reproduction of the analysis presented here.
Zero-phonon-line emission of single molecules for applications in quantum information processing

NASA Astrophysics Data System (ADS)

Kiraz, Alper; Ehrl, M.; Mustecaplioglu, O. E.; Hellerer, T.; Brauchle, C.; Zumbusch, A.

2005-07-01

A single photon source which generates transform limited single photons is highly desirable for applications in quantum optics. Transform limited emission guarantees the indistinguishability of the emitted single photons. This, in turn brings groundbreaking applications in linear optics quantum information processing within an experimental reach. Recently, self-assembled InAs quantum dots and trapped atoms have successfully been demonstrated as such sources for highly indistinguishable single photons. Here, we demonstrate that nearly transform limited zero-phonon-line (ZPL) emission from single molecules can be obtained by using vibronic excitation. Furthermore we report the results of coincidence detection experiments at the output of a Michelson-type interferometer. These experiments reveal Hong-Ou-Mandel correlations as a proof of the indistinguishability of the single photons emitted consecutively from a single molecule. Therefore, single molecules constitute an attractive alternative to single InAs quantum dots and trapped atoms for applications in linear optics quantum information processing. Experiments were performed with a home-built confocal microscope keeping the sample in a superfluid liquid Helium bath at 1.4K. We investigated terrylenediimide (TDI) molecules highly diluted in hexadecane (Shpol'skii matrix). A continuous wave single mode dye laser was used for excitation of vibronic transitions of individual molecules. From the integral fluorescence, the ZPL of single molecules was selected with a spectrally narrow interference filter. The ZPL emission was then sent to a scanning Fabry-Perot interferometer for linewidth measurements or a Michelson-type interferometer for coincidence detection.
DNA of a Human Hepatitis B Virus Candidate

PubMed Central

Robinson, William S.; Clayton, David A.; Greenman, Richard L.

1974-01-01

Particles containing DNA polymerase (Dane particles) were purified from the plasma of chronic carriers of hepatitis B antigen. After a DNA polymerase reaction with purified Dane particle preparations treated with Nonidet P-40 detergent, Dane particle core structures containing radioactive DNA product were isolated by sedimentation in a sucrose density gradient. The radioactive DNA was extracted with sodium dodecyl sulfate and isolated by band sedimentation in a preformed CsCl gradient. Examination of the radioactive DNA band by electron microscopy revealed exclusively circular double-stranded DNA molecules approximately 0.78 μm in length. Identical circular molecules were observed when DNA was isolated by a similar procedure from particles that had not undergone a DNA polymerase reaction. The molecules were completely degraded by DNase 1. When Dane particle core structures were treated with DNase 1 before DNA extraction, only 0.78-μm circular DNA molecules were detected. Without DNase treatment of core structures, linear molecules with lengths between 0.5 and 12 μm, in addition to the 0.78-μm circles were found. These results suggest that the 0.78-μm circular molecules were in a protected position within Dane particle cores and the linear molecules were not within core structures. Length measurements on 225 circular molecules revealed a mean length of 0.78 ± 0.09 μm which would correspond to a molecular weight of around 1.6 × 106. The circular molecules probably serve as primer-template for the DNA polymerase reaction carried out by Dane particle cores. Thermal denaturation and buoyant density measurements on the Dane particle DNA polymerase reaction product revealed a guanosine plus cytosine content of 48 to 49%. Images PMID:4847328
The H+n-C5H12/n-C6H14→H2(v',j')+C5H11/C6H13 reactions: State-to-state dynamics and models of energy disposal

NASA Astrophysics Data System (ADS)

Picconatto, Carl A.; Srivastava, Abneesh; Valentini, James J.

2001-03-01

The rovibrational state distributions for the H2 product of the H+n-C5H12/n-C6H14→H2+C5H11/C6H13 reactions at 1.6 eV collision energy are reported. The results are compared to measurements made on the kinematically and energetically similar H+RH→H2+R (RH=CH4, C2H6, and C3H8) reactions as well as the atom-diatom reactions H+HX→H2+X(HX=HCl, HBr). For the title reactions, as for all the comparison reactions, the product appears in few of the energetically accessible states. This is interpreted as the result of a kinematic constraint on the product translational energy. Characteristic of the H+RH reactions we have previously studied, the title reactions show increasing rotational excitation of the H2 product with increasing vibrational excitation of it, a correlation that gets stronger as the size of the alkane increases. Trends and variations in the product energy disposal are analyzed and explained by a localized reaction model. This model predicates a truncation of the opacity function due to competing reactive sites in the polyatomic alkane reactant, and a relaxation of the otherwise tight coupling of energy and angular momentum conservation, because the polyatomic alkyl radical product is a sink for angular momentum.
Simulation of homogeneous condensation of small polyatomic systems in high pressure supersonic nozzle flows using Bhatnagar-Gross-Krook model

NASA Astrophysics Data System (ADS)

Kumar, Rakesh; Levin, Deborah A.

2011-03-01

In the present work, we have simulated the homogeneous condensation of carbon dioxide and ethanol using the Bhatnagar-Gross-Krook based approach. In an earlier work of Gallagher-Rogers et al. [J. Thermophys. Heat Transfer 22, 695 (2008)], it was found that it was not possible to simulate condensation experiments of Wegener et al. [Phys. Fluids 15, 1869 (1972)] using the direct simulation Monte Carlo method. Therefore, in this work, we have used the statistical Bhatnagar-Gross-Krook approach, which was found to be numerically more efficient than direct simulation Monte Carlo method in our previous studies [Kumar et al., AIAA J. 48, 1531 (2010)], to model homogeneous condensation of two small polyatomic systems, carbon dioxide and ethanol. A new weighting scheme is developed in the Bhatnagar-Gross-Krook framework to reduce the computational load associated with the study of homogeneous condensation flows. The solutions obtained by the use of the new scheme are compared with those obtained by the baseline Bhatnagar-Gross-Krook condensation model (without the species weighting scheme) for the condensing flow of carbon dioxide in the stagnation pressure range of 1-5 bars. Use of the new weighting scheme in the present work makes the simulation of homogeneous condensation of ethanol possible. We obtain good agreement between our simulated predictions for homogeneous condensation of ethanol and experiments in terms of the point of condensation onset and the distribution of mass fraction of ethanol condensed along the nozzle centerline.
Analysis of twenty five impurities in uranium matrix by ICP-MS with iron measurement optimized by using reaction collision cell, cold plasma or medium resolution.

PubMed

Quemet, Alexandre; Brennetot, Rene; Chevalier, Emilie; Prian, Edwina; Laridon, Anne-Laure; Mariet, Clarisse; Fichet, Pascal; Laszak, Ivan; Goutelard, Florence

2012-09-15

An analytical procedure was developed to determine the concentration of 25 impurities (Li, Be, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Zr, Mo, Ag, Cd, In, Sm, Eu, Gd, Dy, W, Pb, Bi and Th) in a uranium matrix using the quadrupole inductively coupled plasma mass spectrometry (Q-ICP-MS). The dissolution of U(3)O(8) powder was made with a mixture of hydrochloric acid and nitric acid. Then, a selective separation of uranium using the UTEVA column was used before measurement by Q-ICP-MS. The procedure developed was verified using the Certified Reference Material "Morille". The analytical results agree well except for 5 elements where values are underestimated (Li, Be, In, Pb and Bi). Among the list of impurities, iron was particularly investigated because it is well known that this element possesses a polyatomic interference that increases the detection limit. A comparison between iron detection limits obtained with different methods was performed. Iron polyatomic interference was at least reduced, or at best entirely resolved in some cases, by using the cold plasma or the collision/reaction cell with several gases (He, NH(3) and CH(4)). High-resolution ICP-MS was used to compare the results obtained. A detection limit as low as 8 ng L(-1) was achieved. Copyright © 2012 Elsevier B.V. All rights reserved.
Identification and Characterization of Circular RNAs As a New Class of Putative Biomarkers in Human Blood

PubMed Central

Peters, Oliver; Rajewsky, Nikolaus

2015-01-01

Covalently closed circular RNA molecules (circRNAs) have recently emerged as a class of RNA isoforms with widespread and tissue specific expression across animals, oftentimes independent of the corresponding linear mRNAs. circRNAs are remarkably stable and sometimes highly expressed molecules. Here, we sequenced RNA in human peripheral whole blood to determine the potential of circRNAs as biomarkers in an easily accessible body fluid. We report the reproducible detection of thousands of circRNAs. Importantly, we observed that hundreds of circRNAs are much higher expressed than corresponding linear mRNAs. Thus, circRNA expression in human blood reveals and quantifies the activity of hundreds of coding genes not accessible by classical mRNA specific assays. Our findings suggest that circRNAs could be used as biomarker molecules in standard clinical blood samples. PMID:26485708
DNA recombination activity in soybean mitochondria.

PubMed

Manchekar, Medha; Scissum-Gunn, Karyn; Song, Daqing; Khazi, Fayaz; McLean, Stephanie L; Nielsen, Brent L

2006-02-17

Mitochondrial genomes in higher plants are much larger and more complex as compared to animal mitochondrial genomes. There is growing evidence that plant mitochondrial genomes exist predominantly as a collection of linear and highly branched DNA molecules and replicate by a recombination-dependent mechanism. However, biochemical evidence of mitochondrial DNA (mtDNA) recombination activity in plants has previously been lacking. We provide the first report of strand-invasion activity in plant mitochondria. Similar to bacterial RecA, this activity from soybean is dependent on the presence of ATP and Mg(2+). Western blot analysis using an antibody against the Arabidopsis mitochondrial RecA protein shows cross-reaction with a soybean protein of about 44 kDa, indicating conservation of this protein in at least these two plant species. mtDNA structure was analyzed by electron microscopy of total soybean mtDNA and molecules recovered after field-inversion gel electrophoresis (FIGE). While most molecules were found to be linear, some molecules contained highly branched DNA structures and a small but reproducible proportion consisted of circular molecules (many with tails) similar to recombination intermediates. The presence of recombination intermediates in plant mitochondria preparations is further supported by analysis of mtDNA molecules by 2-D agarose gel electrophoresis, which indicated the presence of complex recombination structures along with a considerable amount of single-stranded DNA. These data collectively provide convincing evidence for the occurrence of homologous DNA recombination in plant mitochondria.
Nanoscale Trapping and Squeeze-Out of Confined Alkane Monolayers.

PubMed

Gosvami, N N; O'Shea, S J

2015-12-01

We present combined force curve and conduction atomic force microscopy (AFM) data for the linear alkanes CnH2n+2 (n = 10, 12, 14, 16) confined between a gold-coated AFM tip and a graphite surface. Solvation layering is observed in the force curves for all liquids, and conduction AFM is used to study in detail the removal of the confined (mono)layer closest to the graphite surface. The squeeze-out behavior of the monolayer can be very different depending upon the temperature. Below the monolayer melting transition temperatures the molecules are in an ordered state on the graphite surface, and fast and complete removal of the confined molecules is observed. However, above the melting transition temperature the molecules are in a disordered state, and even at large applied pressure a few liquid molecules are trapped within the tip-sample contact zone. These findings are similar to a previous study for branched alkanes [ Gosvami Phys. Rev. Lett. 2008, 100, 076101 ], but the observation for the linear alkane homologue series demonstrates clearly the dependence of the squeeze-out and trapping on the state of the confined material.
Prediction of octanol-water partition coefficients of organic compounds by multiple linear regression, partial least squares, and artificial neural network.

PubMed

Golmohammadi, Hassan

2009-11-30

A quantitative structure-property relationship (QSPR) study was performed to develop models those relate the structure of 141 organic compounds to their octanol-water partition coefficients (log P(o/w)). A genetic algorithm was applied as a variable selection tool. Modeling of log P(o/w) of these compounds as a function of theoretically derived descriptors was established by multiple linear regression (MLR), partial least squares (PLS), and artificial neural network (ANN). The best selected descriptors that appear in the models are: atomic charge weighted partial positively charged surface area (PPSA-3), fractional atomic charge weighted partial positive surface area (FPSA-3), minimum atomic partial charge (Qmin), molecular volume (MV), total dipole moment of molecule (mu), maximum antibonding contribution of a molecule orbital in the molecule (MAC), and maximum free valency of a C atom in the molecule (MFV). The result obtained showed the ability of developed artificial neural network to prediction of partition coefficients of organic compounds. Also, the results revealed the superiority of ANN over the MLR and PLS models. Copyright 2009 Wiley Periodicals, Inc.

Acenes, Heteroacenes and Analogous Molecules for Organic Photovoltaic and Field Effect Transistor Applications

NASA Astrophysics Data System (ADS)

Granger, Devin Benjamin

Polycyclic aromatic hydrocarbons composed of benzenoid rings fused in a linear fashion comprise the class of compounds known as acenes. The structures containing three to six ring fusions are brightly colored and possess band gaps and charge transport efficiencies sufficient for semiconductor applications. These molecules have been investigated throughout the past several decades to assess their optoelectronic properties. The absorption, emission and charge transport properties of this series of molecules has been studied extensively to elucidate structure-property relationships. A wide variety of analogous molecules, incorporating heterocycles in place of benzenoid rings, demonstrate similar properties to the parent compounds and have likewise been investigated. Functionalization of acene compounds by placement of groups around the molecule affects the way in which molecules interact in the solid state, in addition to the energetics of the molecule. The use of electron donating or electron withdrawing groups affects the frontier molecular orbitals and thus affects the optical and electronic gaps of the molecules. The use of bulky side groups such as alkylsilylethynyl groups allows for crystal engineering of molecular aggregates, and changing the volume and dimensions of the alkylsilyl groups affects the intermolecular interactions and thus changes the packing motif. In chapter 2, a series of tetracene and pentacene molecules with strongly electron withdrawing groups is described. The investigation focuses on the change in energetics of the frontier molecular orbitals between the base acene and the nitrile and dicyanovinyl derivatives as well as the differences between the pentacene and tetracene molecules. The differences in close packing motifs through use of bulky alkylsilylethynyl groups is also discussed in relation to electron acceptor material design and bulk heterojunction organic photovoltaic characteristics. Chapter 3 focuses on molecular acceptor and donor molecules for bulk heterojunction organic photovoltaics based on anthrathiophene and benzo[1,2-b:4,5-b']dithiophene central units like literature molecules containing fluorene and dithieno[2,3-b:2',3'-d]silole cores. The synthetic strategies of developing reduced symmetry benzo[1,2-b:4,5-b']dithiophene to study the effect of substitution around the central unit is also described. The optical and electronic properties of the donors and acceptors are described along with the performance and characteristics of devices employing these molecules. The final two data chapters focus on new nitrogen containing polycyclic hydrocarbons containing indolizine and (2.2.2) cyclazine units. The optical, electronic and other physical properties of these molecules are explored, in addition to the synthetic strategies for incorporating the indolizine and cyclazine units. By use of alkylsilylethynyl groups, crystal engineering was investigated for the benzo[2,3-b:5,6-b']diindolizine chromophore described in chapter 4 to target the 2-D "brick-work" packing motif for application in field effect transistor devices. Optical and electronic properties of the cyclazine end-capped acene molecules described in chapter 5 were investigated and described in relation to the base acene molecules. In both cases, density functional theory calculations were conducted to better understand unexpected optical properties of these molecules, which are like the linear acene series despite the non-linear attachment.
Linearization of calibration curves by aerosol carrier effect of CCl 4 vapor in electrothermal vaporization inductively coupled plasma mass spectrometry

NASA Astrophysics Data System (ADS)

Kántor, Tibor; de Loos-Vollebregt, Margaretha T. C.

2005-03-01

Carbon tetrachloride vapor as gaseous phase modifier in a graphite furnace electrothermal vaporizer (GFETV) converts heavy volatile analyte forms to volatile and medium volatile chlorides and produces aerosol carrier effect, the latter being a less generally recognized benefit. However, the possible increase of polyatomic interferences in inductively coupled plasma mass spectrometry (GFETV-ICP-MS) by chlorine and carbon containing species due to CCl 4 vapor introduction has been discouraging with the use of low resolution, quadrupole type MS equipment. Being aware of this possible handicap, it was aimed at to investigate the feasibility of the use of this halogenating agent in ICP-MS with regard of possible hazards to the instrument, and also to explore the advantages under these specific conditions. With sample gas flow (inner gas flow) rate not higher than 900 ml min -1 Ar in the torch and 3 ml min -1 CCl 4 vapor flow rate in the furnace, the long-term stability of the instrument was ensured and the following benefits by the halocarbon were observed. The non-linearity error (defined in the text) of the calibration curves (signal versus mass functions) with matrix-free solution standards was 30-70% without, and 1-5% with CCl 4 vapor introduction, respectively, at 1 ng mass of Cu, Fe, Mn and Pb analytes. The sensitivity for these elements increased by 2-4-fold with chlorination, while the relative standard deviation (RSD) was essentially the same (2-5%) for the two cases in comparison. A vaporization temperature of 2650 °C was required for Cr in Ar atmosphere, while 2200 °C was sufficient in Ar + CCl 4 atmosphere to attain complete vaporization. Improvements in linear response and sensitivity were the highest for this least volatile element. The pyrolytic graphite layer inside the graphite tube was protected by the halocarbon, and tube life time was further increased by using traces of hydrocarbon vapor in the external sheath gas of the graphite furnace. Details of the modification of the gas supply for HGA-600MS furnace and the design of the volatilization device are described.
Adsorption of methyl green on montmorillonite

NASA Astrophysics Data System (ADS)

Margulies, Leon; Rozen, Harel

1986-03-01

Adsorption of the dye methyl green (MG) on Na -montmorillonite (Clay) takes place through a cation exchange mechanism. At low and high MG loads, each MG molecule replaces approximately two and one Na + ions, respectively. Interactions between MG and Clay were studied using visible absorption and FTIR spectroscopies, and the orientation of the adsorbed molecules were determined by infrared linear dichroism and X-ray powder diffraction. The dye molecules are preferentially oriented with their plane parallel to the clay surface. The influence of MG load on the adsorption of two additional organic molecules, benzyl benzoate and benzophenone, was also studied.
Structural Design and Photochemical Preparation of Ultrathin Molecular Film Materials

DTIC Science & Technology

2006-12-01

tetracene and pentacene that have great potential as organic semiconducting materials, have been determined. Overall, we have gained to great extend a...layer of linear acenes, molecules such as tetracene and pentacene that have great potential as organic semiconducting materials, have been determined...intermolecular interaction of mono- and multi-layer linear acenes on metal A systematic study of adsorption of linear acenes, from benzene to pentacene , on metal
A scale-bridging modeling approach for anisotropic organic molecules at patterned semiconductor surfaces

NASA Astrophysics Data System (ADS)

Kleppmann, Nicola; Klapp, Sabine H. L.

2015-02-01

Hybrid systems consisting of organic molecules at inorganic semiconductor surfaces are gaining increasing importance as thin film devices for optoelectronics. The efficiency of such devices strongly depends on the collective behavior of the adsorbed molecules. In the present paper, we propose a novel, coarse-grained model addressing the condensed phases of a representative hybrid system, that is, para-sexiphenyl (6P) at zinc-oxide (ZnO). Within our model, intermolecular interactions are represented via a Gay-Berne potential (describing steric and van-der-Waals interactions) combined with the electrostatic potential between two linear quadrupoles. Similarly, the molecule-substrate interactions include a coupling between a linear molecular quadrupole to the electric field generated by the line charges characterizing ZnO(10-10). To validate our approach, we perform equilibrium Monte Carlo simulations, where the lateral positions are fixed to a 2D lattice, while the rotational degrees of freedom are continuous. We use these simulations to investigate orientational ordering in the condensed state. We reproduce various experimentally observed features such as the alignment of individual molecules with the line charges on the surface, the formation of a standing uniaxial phase with a herringbone structure, as well as the formation of a lying nematic phase.
Energy level alignment of self-assembled linear chains of benzenediamine on Au(111) from first principles

NASA Astrophysics Data System (ADS)

Li, Guo; Rangel, Tonatiuh; Liu, Zhen-Fei; Cooper, Valentino R.; Neaton, Jeffrey B.

2016-03-01

Using density functional theory (DFT) with a van der Waals density functional, we calculate the adsorption energetics and geometry of benzenediamine (BDA) molecules on Au(111) surfaces. Our results demonstrate that the reported self-assembled linear chain structure of BDA, stabilized via hydrogen bonds between amine groups, is energetically favored over previously studied monomeric phases. Moreover, using a model, which includes nonlocal polarization effects from the substrate and the neighboring molecules and incorporates many-body perturbation theory calculations within the GW approximation, we obtain approximate self-energy corrections to the DFT highest occupied molecular orbital (HOMO) energy associated with BDA adsorbate phases. We find that, independent of coverage, the HOMO energy of the linear chain phase is lower relative to the Fermi energy than that of the monomer phase, and in good agreement with values measured with ultraviolet photoelectron spectroscopy and x-ray photoelectron spectroscopy.
Sequential Excitation Preparation of Molecular Energy Levels with Special Structural and Chemical Properties.

DTIC Science & Technology

1986-01-06

D.E. Reisner, and P.H. Vaccaro, pp. 393-404 in Lasers as Reactants and Probes in Chemistry, (eds. W.M. Jackson and A.B. Harvey) Howard University Press...as Reactants and Probes in Chemistry, Howard University (May 1982). 4. J.L. Kinsey, "An Outsider’s View of the Spectroscopy of Polyatomic Systems...Kinsey, C. Kittrell, D.E. Reisner, and P.H. Vaccaro, pp. 393-404 in Lasers as Reactants and Probes in Chemistry (eds. W.M. Jackson and A.B. Harvey), Howard
Diffusion of isolated DNA molecules: dependence on length and topology.

PubMed

Robertson, Rae M; Laib, Stephan; Smith, Douglas E

2006-05-09

The conformation and dynamics of circular polymers is a subject of considerable theoretical and experimental interest. DNA is an important example because it occurs naturally in different topological states, including linear, relaxed circular, and supercoiled circular forms. A fundamental question is how the diffusion coefficients of isolated polymers scale with molecular length and how they vary for different topologies. Here, diffusion coefficients D for relaxed circular, supercoiled, and linear DNA molecules of length L ranging from approximately 6 to 290 kbp were measured by tracking the Brownian motion of single molecules. A topology-independent scaling law D approximately L(-nu) was observed with nu(L) = 0.571 +/- 0.014, nu(C) = 0.589 +/- 0.018, and nu(S) = 0.571 +/- 0.057 for linear, relaxed circular, and supercoiled DNA, respectively, in good agreement with the scaling exponent of nu congruent with 0.588 predicted by renormalization group theory for polymers with significant excluded volume interactions. Our findings thus provide evidence in support of several theories that predict an effective diameter of DNA much greater than the Debye screening length. In addition, the measured ratio D(Circular)/D(Linear) = 1.32 +/- 0.014 was closer to the value of 1.45 predicted by using renormalization group theory than the value of 1.18 predicted by classical Kirkwood hydrodynamic theory and agreed well with a value of 1.31 predicted when incorporating a recently proposed expression for the radius of gyration of circular polymers into the Zimm model.
Self-assembled nanostructures of linear arylacetylenes and their aza-substituted analogues

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

Xu, Jia-Ju; Department of Physics and Materials Science and Centre of Super Diamond and Advanced Films; Yang, Xiong-Bo

2016-06-15

A series of linear phenylene ethynylene molecules have been synthesized, and aza-substitution has been used as a strategy to fine-tune the properties of the molecules. All the compounds exhibited pure blue emission both in solution and solid state, and fluorescence quantum yields as high as 0.66, 0.63 and 0.82 were found in chloroform solutions. The well-defined nanostructures such as quasi-cubes, cubes and rods were fabricated by self-assembly method from these compounds. The photophysical properties and aggregation behavior of self-assembled structures were analyzed in detail. The morphology as well as photophysical properties of these nanostructures have been tuned with selective requirements.
Unraveling secrets of telomeres: one molecule at a time

PubMed Central

Lin, Jiangguo; Kaur, Parminder; Countryman, Preston; Opresko, Patricia L.; Wang, Hong

2016-01-01

Telomeres play important roles in maintaining the stability of linear chromosomes. Telomere maintenance involves dynamic actions of multiple proteins interacting with long repetitive sequences and complex dynamic DNA structures, such as G-quadruplexes, T-loops and t-circles. Given the heterogeneity and complexity of telomeres, single-molecule approaches are essential to fully understand the structure-function relationships that govern telomere maintenance. In this review, we present a brief overview of the principles of single-molecule imaging and manipulation techniques. We then highlight results obtained from applying these single-molecule techniques for studying structure, dynamics and functions of G-quadruplexes, telomerase, and shelterin proteins. PMID:24569170
Continuous approximation for interaction energy of adamantane encapsulated inside carbon nanotubes

NASA Astrophysics Data System (ADS)

Baowan, Duangkamon; Hill, James M.; Bacsa, Wolfgang

2018-02-01

The interaction energy for two adjacent adamantane molecules and that of adamantane molecules encapsulated inside carbon nanotubes are investigated considering only dipole-dipole induced interaction. The Lennard-Jones potential and the continuous approximation are utilised to derive analytical expressions for these interaction energies. The equilibrium distance 3.281 Å between two adamantane molecules is determined. The smallest carbon nanotube radius b0 that can encapsulate the adamantane molecule and the radius of the tube bmax that gives the maximum suction energy, linearly depend on the adamantane radius, are calculated. For larger diameter tubes, the off axis position has been calculated, and equilibrium distance between molecule and tube wall is found to be close to the interlayer spacing in graphene.
Monte-Carlo simulations of a coarse-grained model for α-oligothiophenes

NASA Astrophysics Data System (ADS)

Almutairi, Amani; Luettmer-Strathmann, Jutta

The interfacial layer of an organic semiconductor in contact with a metal electrode has important effects on the performance of thin-film devices. However, the structure of this layer is not easy to model. Oligothiophenes are small, π-conjugated molecules with applications in organic electronics that also serve as small-molecule models for polythiophenes. α-hexithiophene (6T) is a six-ring molecule, whose adsorption on noble metal surfaces has been studied extensively (see, e.g., Ref.). In this work, we develop a coarse-grained model for α-oligothiophenes. We describe the molecules as linear chains of bonded, discotic particles with Gay-Berne potential interactions between non-bonded ellipsoids. We perform Monte Carlo simulations to study the structure of isolated and adsorbed molecules
Table 137. H2 16O (H16OH): Line position and intensity for rotational transitions (060)-(060) in the range 757-934 cm-1

NASA Astrophysics Data System (ADS)

Guelachvili, G.; Picqué, N.

This document is part of Subvolume C 'Non-linear Triatomic Molecules', Part 1 'H2O (HOH)', Part α'H2 16O (H16OH)' of Volume 20 'Molecular Constants Mostly from Infrared Spectroscopy' of Landolt-Börnstein - Group II 'Molecules and Radicals'.
Nanopore analysis of polymers in solution.

NASA Astrophysics Data System (ADS)

Deamer, David

2002-03-01

Nanopores represent a novel approach for investigating macromolecules in solution. Polymers that have been analyzed by this technique include polyethylene glycol (PEG), certain proteins and nucleic acids. The a-hemolysin pore inserted into lipid bilayers provides continuous non-gated ion current through a pore diameter of approximately 1.5 - 2 nm. Nucleic acid molecules can be driven through the pore by imposing a voltage across the supporting membrane. Single stranded, but not double stranded nucleic acids pass through in strict linear sequence from one end of the molecule to the other. While in the pore, the molecule reduces ionic current, and properties of the ionic current blockade such as duration, mean amplitude and modulations of amplitude provide information about structure and composition of the nucleic acid. For a given molecular species, the duration of the blockade is a function of chain length, and the rate of blockades is linearly related to concentration. More recent studies have shown that the a-hemolysin nanopore can discriminate between synthetic DNA molecules differing by a single base pair or even a single nucleotide. These results indicate that a nanopore may have the resolution required for nucleic acid sequencing applications.
Interplay between Self-Assembled Structures and Energy Level Alignment of Benzenediamine on Au(111) Surfaces

NASA Astrophysics Data System (ADS)

Li, Guo; Neaton, Jeffrey

2015-03-01

Using van der Waals-corrected density functional theory (DFT) calculations, we study the adsorption of benzene-diamine (BDA) molecules on Au(111) surfaces. We find that at low surface coverage, the adsorbed molecules prefer to stay isolated from each other in a monomer phase, due to the inter-molecular dipole-dipole repulsions. However, when the coverage rises above a critical value of 0.9nm-2, the adsorbed molecules aggregate into linear structures via hydrogen bonding between amine groups, consistent with recent experiments [Haxton, Zhou, Tamblyn, et al, Phys. Rev. Lett. 111, 265701 (2013)]. Moreover, we find that these linear structures at high density considerably reduces the Au work function (relative to a monomer phase). Due to reduced surface polarization effects, we estimate that the resonance energy of the highest occupied molecular orbital of the adsorbed BDA molecule relative to the Au Fermi level is significantly lower than the monomer phase by more than 0.5 eV, consistent with the experimental measurements [DellAngela, Kladnik, and Cossaro, et al., Nano Lett. 10, 2470 (2010)]. This work supported by DOE (the JCAP under Award Number DE-SC000499 and the Molecular Foundry of LBNL), and computational resources provided by NERSC.
ICP-MS multielemental determination of metals potentially released from dental implants and articular prostheses in human biological fluids.

PubMed

Sarmiento-González, Alejandro; Marchante-Gayón, Juan Manuel; Tejerina-Lobo, José María; Paz-Jiménez, José; Sanz-Medel, Alfredo

2005-06-01

A sector field high-resolution (HR)-ICP-MS and an octapole reaction system (ORS)-ICP-MS have been compared for the simultaneous determination of traces of metals (Ti, V, Cr, Co, Ni, and Mo) released from dental implants and articular prostheses in human biological fluids. Optimum sample treatments were evaluated to minimize matrix effects in urine and whole blood. Urine samples were diluted tenfold with ultrapure water, whereas whole blood samples were digested with high-purity nitric acid and hydrogen peroxide and finally diluted tenfold with ultrapure water. In both matrices, internal standardization (Ga and Y) was employed to avoid potential matrix interferences and ICP-MS signal drift. Spectral interferences arising from the plasma gases or the major components of urine and whole blood were identified by (HR)-ICP-MS at 3,000 resolving power. The capabilities of (HR)-ICP-MS and (ORS)-ICP-MS for the removal of such spectral interferences were evaluated and compared. Results indicate that polyatomic interferences, which hamper the determination of such metallic elements in these biological samples, could be overcome by using a resolving power of 3,000. Using (ORS)-ICP-MS, all those elements could be quantified except Ti and V (due to the polyatomic ions 31P16O and 35Cl16O, respectively). The accuracy of the proposed methodologies by (HR)- and (ORS)-ICP-MS was checked against two reference materials. Good agreement between the given values and the concentrations obtained for all the analytes under scrutiny was found except for Ti and V when analyzed by (ORS)-ICP-MS.
Prominent mitochondrial DNA recombination intermediates in human heart muscle.

PubMed

Kajander, O A; Karhunen, P J; Holt, I J; Jacobs, H T

2001-11-01

Recombination intermediates containing four-way (Holliday) junctions are generated during DNA repair and replication in many systems, including yeast mitochondrial DNA (mtDNA). In contrast, convincing evidence for recombination in mammalian mtDNA is lacking. We have used two-dimensional agarose-gel electrophoresis to analyse non-linear forms of mtDNA in human heart muscle. Replication intermediates from both the coupled and strand-asynchronous mtDNA replication pathways were detected. An additional class of non-linear molecules, with the electrophoretic properties of four-way junctions, was also prominent. These molecules were insensitive to topoisomerase I or RNase H, but were diminished by branch migration or RuvC treatment. Junctional molecules were detected in all regions of the mitochondrial genome, were found in myocardial DNA from young and old adults, but were present at lower levels in skeletal muscle and placenta. We suggest that they could represent intermediates of mtDNA repair, given their prevalence in the oxyradical-rich environment of heart muscle mitochondria.
In silico screening of drug-membrane thermodynamics reveals linear relations between bulk partitioning and the potential of mean force

NASA Astrophysics Data System (ADS)

Menichetti, Roberto; Kanekal, Kiran H.; Kremer, Kurt; Bereau, Tristan

2017-09-01

The partitioning of small molecules in cell membranes—a key parameter for pharmaceutical applications—typically relies on experimentally available bulk partitioning coefficients. Computer simulations provide a structural resolution of the insertion thermodynamics via the potential of mean force but require significant sampling at the atomistic level. Here, we introduce high-throughput coarse-grained molecular dynamics simulations to screen thermodynamic properties. This application of physics-based models in a large-scale study of small molecules establishes linear relationships between partitioning coefficients and key features of the potential of mean force. This allows us to predict the structure of the insertion from bulk experimental measurements for more than 400 000 compounds. The potential of mean force hereby becomes an easily accessible quantity—already recognized for its high predictability of certain properties, e.g., passive permeation. Further, we demonstrate how coarse graining helps reduce the size of chemical space, enabling a hierarchical approach to screening small molecules.
Chemistry of anthracene-acetylene oligomers XXV: on-surface chirality of a self-assembled molecular network of a fan-blade-shaped anthracene-acetylene macrocycle with a long alkyl chain.

PubMed

Tsuya, Takuya; Iritani, Kohei; Tahara, Kazukuni; Tobe, Yoshito; Iwanaga, Tetsuo; Toyota, Shinji

2015-03-27

An anthracene cyclic dimer with two different linkers and a dodecyl group was synthesized by means of coupling reactions. The calculated structure had a planar macrocyclic π core and a linear alkyl chain. Scanning tunneling microscopy observations at the 1-phenyloctane/graphite interface revealed that the molecules formed a self-assembled monolayer that consisted of linear striped bright and dark bands. In each domain, the molecular network consisted of either Re or Si molecules that differed in the two-dimensional chirality about the macrocyclic faces, which led to a unique conglomerate-type self-assembly. The molecular packing mode and the conformation of the alkyl chains are discussed in terms of the intermolecular interactions and the interactions between the molecules and the graphite surface with the aid of MM3 simulations of a model system. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Functional helicoidal model of DNA molecule with elastic nonlinearity

NASA Astrophysics Data System (ADS)

Tseytlin, Y. M.

2013-06-01

We constructed a functional DNA molecule model on the basis of a flexible helicoidal sensor, specifically, a pretwisted hollow nano-strip. We study in this article the helicoidal nano- sensor model with a pretwisted strip axial extension corresponding to the overstretching transition of DNA from dsDNA to ssDNA. Our model and the DNA molecule have similar geometrical and nonlinear mechanical features unlike models based on an elastic rod, accordion bellows, or an imaginary combination of "multiple soft and hard linear springs", presented in some recent publications.

Absorption of Deuterium Fluoride Laser Radiation by the Atmosphere

DTIC Science & Technology

1976-04-01

30 lines, and it would have been prohibitively costly in terms of time and money to measure the ab- sorption on all lines. McClatchey, et al.[3...linear molecule (N2O, CO2, CO) Herzberg [5] gives as an approximation 14 ^ Vi ~_ i’: (45) so that (47) qR(T) hcB V. (ln\\ 1.0 For asymmetric...top molecules (H20, 03) Herzberg [5] gives as an approximation (48) so that ABC \\hc; (49) ±-^f) For spherical top molecules (CH4) Herzberg [5
Treatment of charge singularities in implicit solvent models.

PubMed

Geng, Weihua; Yu, Sining; Wei, Guowei

2007-09-21

This paper presents a novel method for solving the Poisson-Boltzmann (PB) equation based on a rigorous treatment of geometric singularities of the dielectric interface and a Green's function formulation of charge singularities. Geometric singularities, such as cusps and self-intersecting surfaces, in the dielectric interfaces are bottleneck in developing highly accurate PB solvers. Based on an advanced mathematical technique, the matched interface and boundary (MIB) method, we have recently developed a PB solver by rigorously enforcing the flux continuity conditions at the solvent-molecule interface where geometric singularities may occur. The resulting PB solver, denoted as MIBPB-II, is able to deliver second order accuracy for the molecular surfaces of proteins. However, when the mesh size approaches half of the van der Waals radius, the MIBPB-II cannot maintain its accuracy because the grid points that carry the interface information overlap with those that carry distributed singular charges. In the present Green's function formalism, the charge singularities are transformed into interface flux jump conditions, which are treated on an equal footing as the geometric singularities in our MIB framework. The resulting method, denoted as MIBPB-III, is able to provide highly accurate electrostatic potentials at a mesh as coarse as 1.2 A for proteins. Consequently, at a given level of accuracy, the MIBPB-III is about three times faster than the APBS, a recent multigrid PB solver. The MIBPB-III has been extensively validated by using analytically solvable problems, molecular surfaces of polyatomic systems, and 24 proteins. It provides reliable benchmark numerical solutions for the PB equation.
Applications of a general random-walk theory for confined diffusion.

PubMed

Calvo-Muñoz, Elisa M; Selvan, Myvizhi Esai; Xiong, Ruichang; Ojha, Madhusudan; Keffer, David J; Nicholson, Donald M; Egami, Takeshi

2011-01-01

A general random walk theory for diffusion in the presence of nanoscale confinement is developed and applied. The random-walk theory contains two parameters describing confinement: a cage size and a cage-to-cage hopping probability. The theory captures the correct nonlinear dependence of the mean square displacement (MSD) on observation time for intermediate times. Because of its simplicity, the theory also requires modest computational requirements and is thus able to simulate systems with very low diffusivities for sufficiently long time to reach the infinite-time-limit regime where the Einstein relation can be used to extract the self-diffusivity. The theory is applied to three practical cases in which the degree of order in confinement varies. The three systems include diffusion of (i) polyatomic molecules in metal organic frameworks, (ii) water in proton exchange membranes, and (iii) liquid and glassy iron. For all three cases, the comparison between theory and the results of molecular dynamics (MD) simulations indicates that the theory can describe the observed diffusion behavior with a small fraction of the computational expense. The confined-random-walk theory fit to the MSDs of very short MD simulations is capable of accurately reproducing the MSDs of much longer MD simulations. Furthermore, the values of the parameter for cage size correspond to the physical dimensions of the systems and the cage-to-cage hopping probability corresponds to the activation barrier for diffusion, indicating that the two parameters in the theory are not simply fitted values but correspond to real properties of the physical system.
Atomic and polyatomic molecules at metal surfaces studied by synchrotron far-IR RAIRS

NASA Astrophysics Data System (ADS)

Raval, Rasmita; Roberts, Adam J.; Williams, Jamie; Nunney, Timothy S.; Surman, Mark

1997-10-01

Far-IR Reflection Absorption Infrared Spectroscopy (RAIRS) has been used to probe submonolayers of adsorbates created under clean controlled conditions on small area single crystal surfaces, using the newly commissioned Daresbury 13.3 Far-IR synchrotron beamline. Adsorbed formate species on Cu(110) were studied as an example of an adsorbate for which a large structural data-base already exists in the literature from other surface science techniques. Our high resolution Far-IR data has allowed two distinct vCu-O vibrations to be monitored for 0.25 monolayer of formate adsorbed on Cu(110) at 300 K. We rule out a lower symmetry formate complex giving rise to these vibrations and, instead, attribute the two bands to at least two chemically distinct species at the surface, a possibility that has hitherto not been included in the analyses of this system using other techniques. In addition, we also report the first RAIRS spectrum of the vCu-O stretching vibration for adsorbed atomic O on the Cu(110) surface at 300 K. The dissociative adsorption of oxygen, at room temperature, on this surface is known to induce a massive reconstruction of the surface in which `added' rows of Cu-O-Cu strings form on the surface in the [001] direction to give rise to the (1 X 2) missing row structure. The vCu-O vibration frequency is found to be invariant as a function of coverage, suggesting that the chemical nature of the Cu-O-Cu entity remains essentially unaltered during the growth of the reconstructed phase.
Treatment of charge singularities in implicit solvent models

NASA Astrophysics Data System (ADS)

Geng, Weihua; Yu, Sining; Wei, Guowei

2007-09-01

This paper presents a novel method for solving the Poisson-Boltzmann (PB) equation based on a rigorous treatment of geometric singularities of the dielectric interface and a Green's function formulation of charge singularities. Geometric singularities, such as cusps and self-intersecting surfaces, in the dielectric interfaces are bottleneck in developing highly accurate PB solvers. Based on an advanced mathematical technique, the matched interface and boundary (MIB) method, we have recently developed a PB solver by rigorously enforcing the flux continuity conditions at the solvent-molecule interface where geometric singularities may occur. The resulting PB solver, denoted as MIBPB-II, is able to deliver second order accuracy for the molecular surfaces of proteins. However, when the mesh size approaches half of the van der Waals radius, the MIBPB-II cannot maintain its accuracy because the grid points that carry the interface information overlap with those that carry distributed singular charges. In the present Green's function formalism, the charge singularities are transformed into interface flux jump conditions, which are treated on an equal footing as the geometric singularities in our MIB framework. The resulting method, denoted as MIBPB-III, is able to provide highly accurate electrostatic potentials at a mesh as coarse as 1.2Å for proteins. Consequently, at a given level of accuracy, the MIBPB-III is about three times faster than the APBS, a recent multigrid PB solver. The MIBPB-III has been extensively validated by using analytically solvable problems, molecular surfaces of polyatomic systems, and 24 proteins. It provides reliable benchmark numerical solutions for the PB equation.
The Helix Nebula Viewed in HCO+: Large-scale Mapping of the J = 1 → 0 Transition

NASA Astrophysics Data System (ADS)

Zeigler, N. R.; Zack, L. N.; Woolf, N. J.; Ziurys, L. M.

2013-11-01

The J = 1 → 0 transition of HCO+ at 89 GHz has been mapped across the Helix Nebula (NGC 7293) with 70'' spatial resolution (1.68 km s-1 velocity resolution) using the Arizona Radio Observatory 12 m telescope. This work is the first large-scale mapping project of a dense gas tracer (n(H2) ~ 105 cm-3) in old planetary nebulae. Observations of over 200 positions encompassing the classical optical image were conducted with a 3σ noise level of ~20 mK. HCO+ was detected at most positions, often exhibiting multiple velocity components indicative of complex kinematic structures in dense gas. The HCO+ spectra suggest that the Helix is composed of a bipolar, barrel-like structure with red- and blue-shifted halves, symmetric with respect to the central star and oriented ~10° east from the line of sight. A second bipolar, higher velocity outflow exists as well, situated along the direction of the Helix "plumes." The column density of HCO+ across the Helix is N tot ~ 1.5 × 1010-5.0 × 1011 cm-2, with an average value N ave ~ 1 × 1011 cm-2, corresponding to an abundance, relative to H2, of f ~ 1.4 × 10-8. This value is similar to that observed in young PN, and contradicts chemical models, which predict that the abundance of HCO+ decreases with nebular age. This study indicates that polyatomic molecules readily survive the ultraviolet field of the central white dwarf, and can be useful in tracing nebular morphology in the very late stages of stellar evolution.
New developments in theoretical thermochemistry and electronic structure applications in supramolecular chemistry and cluster science

NASA Astrophysics Data System (ADS)

Ramabhadran, Raghunath Ozhapakkam

In a concise display of the power and diversity of electronic structure theory (EST), the work presented herein involves the development of new computational methods to advance the practical utility of quantum chemistry, as well as solving different types of challenging chemical problems by applying existing EST tools. The research presented is highly interdisciplinary in nature and features synergistic collaborations to solve real-life problems such as regulating toxic chemicals and generating alternative sources of energy. In the first chapter of this dissertation, the solution to a long-standing problem in theoretical thermochemistry is accomplished by the development of the automated, chemically intuitive and generalized thermochemical hierarchy, Connectivity-Based Hierarchy (CBH) to accurately predict the thermochemical properties of organic molecules. The extension of the hierarchy to predict the enthalpies of formations of biomonomers such as amino acids is also presented. The development of a computationally efficient protocol to accurately extrapolate to high CCSD(T) energies based on MP2 and DFT energies using CBH is presented in the second chapter, thus merging theoretical thermochemistry with fragment-based methods in quantum chemistry. This merger drastically reduces the computational cost involved in a CCSD(T) calculation, while retaining the impeccable accuracy it offers. The practical utility of the CH hydrogen bond, commonly thought as being too weak to be used in supramolecular applications has been demonstrated by DFT calculations (along with experimental results from the Flood group) in the third chapter. This is accomplished by systematically studying the binding of monoatomic chloride, diatomic and toxic cyanide and the polyatomic bi-fluoride anions for the first time using only CH hydrogen bonds within a triazolophane macrocycle. The fourth chapter contains the introduction of the concept of fluxionality in the chemical reactions of transition metal oxide clusters. This is useful to develop a systematic paradigm for discussing the mechanisms in the reactions of larger transition metal oxide clusters with small molecules. Additionally, DFT calculations (along with experimental results from the C. C. Jarrold group) are shown to be useful to provide new insights on hydrogen liberation from water, thus aiding in the generation of alternative sources of energy.
Solution of the Schrodinger Equation for a Diatomic Oscillator Using Linear Algebra: An Undergraduate Computational Experiment

ERIC Educational Resources Information Center

Gasyna, Zbigniew L.

2008-01-01

Computational experiment is proposed in which a linear algebra method is applied to the solution of the Schrodinger equation for a diatomic oscillator. Calculations of the vibration-rotation spectrum for the HCl molecule are presented and the results show excellent agreement with experimental data. (Contains 1 table and 1 figure.)
Study of gas adsorption on as-produced and modified carbon nanotubes

NASA Astrophysics Data System (ADS)

Rawat, Dinesh Singh

Volumetric adsorption isotherm measurements were used to study the adsorption characteristics of Ethane (C2H6) and Butane (C 4H10) on as-produced single-walled carbon nanotubes. The binding energy of the adsorbed alkane molecule was found to increase with increasing carbon chain length. Two adsorption substeps were obtained for each alkane molecule. However, the size of the high pressure substep was found to be gradually smearing with the increase in size of the adsorbed molecule. This phenomenon is interpreted as size entropy effect for linear molecules. This interpretation was also verified by determining the specific surface area of the substrate using linear molecules of different sizes. Kinetics measurements of alkane adsorption on SWNTs were also conducted and their dependence on the molecular length was determined. Similar adsorption measurements were performed for Argon (Ar) on as-produced single-walled carbon nanotubes and nanotubes that were structurally modified using acid treatment. Enhancement of the sorptive capacity and the presence of two distinct kinetics of gas adsorption verified partial opening of single walled carbon nanotubes as a result of chemical treatment. Mutiwalled carbon nanotubes were exposed to oxygen plasma treatment for varying time periods. Afterwards, adsorption measurements of Methane (CH 4) were conducted on untreated and oxygen plasma treated tubes. The presence of an additional substep, after exposing multiwalled carbon nanotubes to oxygen plasma for varying time periods, suggested progressive cleaning of nanotube surface.
Inhaled corticosteroids in children with persistent asthma: effects on growth.

PubMed

Zhang, Linjie; Prietsch, Sílvio O M; Ducharme, Francine M

2014-07-17

Treatment guidelines for asthma recommend inhaled corticosteroids (ICS) as first-line therapy for children with persistent asthma. Although ICS treatment is generally considered safe in children, the potential systemic adverse effects related to regular use of these drugs have been and continue to be a matter of concern, especially the effects on linear growth. To assess the impact of ICS on the linear growth of children with persistent asthma and to explore potential effect modifiers such as characteristics of available treatments (molecule, dose, length of exposure, inhalation device) and of treated children (age, disease severity, compliance with treatment). We searched the Cochrane Airways Group Specialised Register of trials (CAGR), which is derived from systematic searches of bibliographic databases including CENTRAL, MEDLINE, EMBASE, CINAHL, AMED and PsycINFO; we handsearched respiratory journals and meeting abstracts. We also conducted a search of ClinicalTrials.gov and manufacturers' clinical trial databases to look for potential relevant unpublished studies. The literature search was conducted in January 2014. Parallel-group randomised controlled trials comparing daily use of ICS, delivered by any type of inhalation device for at least three months, versus placebo or non-steroidal drugs in children up to 18 years of age with persistent asthma. Two review authors independently performed study selection, data extraction and assessment of risk of bias in included studies. We conducted meta-analyses using the Cochrane statistical package RevMan 5.2 and Stata version 11.0. We used the random-effects model for meta-analyses. We used mean differences (MDs) and 95% CIs as the metrics for treatment effects. A negative value for MD indicates that ICS have suppressive effects on linear growth compared with controls. We performed a priori planned subgroup analyses to explore potential effect modifiers, such as ICS molecule, daily dose, inhalation device and age of the treated child. We included 25 trials involving 8471 (5128 ICS-treated and 3343 control) children with mild to moderate persistent asthma. Six molecules (beclomethasone dipropionate, budesonide, ciclesonide, flunisolide, fluticasone propionate and mometasone furoate) [corrected] given at low or medium daily doses were used during a period of three months to four to six years. Most trials were blinded and over half of the trials had drop out rates of over 20%.Compared with placebo or non-steroidal drugs, ICS produced a statistically significant reduction in linear growth velocity (14 trials with 5717 participants, MD -0.48 cm/y, 95% CI -0.65 to -0.30, moderate quality evidence) and in the change from baseline in height (15 trials with 3275 participants; MD -0.61 cm/y, 95% CI -0.83 to -0.38, moderate quality evidence) during a one-year treatment period.Subgroup analysis showed a statistically significant group difference between six molecules in the mean reduction of linear growth velocity during one-year treatment (Chi² = 26.1, degrees of freedom (df) = 5, P value < 0.0001). The group difference persisted even when analysis was restricted to the trials using doses equivalent to 200 μg/d hydrofluoroalkane (HFA)-beclomethasone. Subgroup analyses did not show a statistically significant impact of daily dose (low vs medium), inhalation device or participant age on the magnitude of ICS-induced suppression of linear growth velocity during a one-year treatment period. However, head-to-head comparisons are needed to assess the effects of different drug molecules, dose, inhalation device or patient age. No statistically significant difference in linear growth velocity was found between participants treated with ICS and controls during the second year of treatment (five trials with 3174 participants; MD -0.19 cm/y, 95% CI -0.48 to 0.11, P value 0.22). Of two trials that reported linear growth velocity in the third year of treatment, one trial involving 667 participants showed similar growth velocity between the budesonide and placebo groups (5.34 cm/y vs 5.34 cm/y), and another trial involving 1974 participants showed lower growth velocity in the budesonide group compared with the placebo group (MD -0.33 cm/y, 95% CI -0.52 to -0.14, P value 0.0005). Among four trials reporting data on linear growth after treatment cessation, three did not describe statistically significant catch-up growth in the ICS group two to four months after treatment cessation. One trial showed accelerated linear growth velocity in the fluticasone group at 12 months after treatment cessation, but there remained a statistically significant difference of 0.7 cm in height between the fluticasone and placebo groups at the end of the three-year trial.One trial with follow-up into adulthood showed that participants of prepubertal age treated with budesonide 400 μg/d for a mean duration of 4.3 years had a mean reduction of 1.20 cm (95% CI -1.90 to -0.50) in adult height compared with those treated with placebo. Regular use of ICS at low or medium daily doses is associated with a mean reduction of 0.48 cm/y in linear growth velocity and a 0.61-cm change from baseline in height during a one-year treatment period in children with mild to moderate persistent asthma. The effect size of ICS on linear growth velocity appears to be associated more strongly with the ICS molecule than with the device or dose (low to medium dose range). ICS-induced growth suppression seems to be maximal during the first year of therapy and less pronounced in subsequent years of treatment. However, additional studies are needed to better characterise the molecule dependency of growth suppression, particularly with newer molecules (mometasone, ciclesonide), to specify the respective role of molecule, daily dose, inhalation device and patient age on the effect size of ICS, and to define the growth suppression effect of ICS treatment over a period of several years in children with persistent asthma.
Linear alkane polymerization on a gold surface.

PubMed

Zhong, Dingyong; Franke, Jörn-Holger; Podiyanachari, Santhosh Kumar; Blömker, Tobias; Zhang, Haiming; Kehr, Gerald; Erker, Gerhard; Fuchs, Harald; Chi, Lifeng

2011-10-14

In contrast to the many methods of selectively coupling olefins, few protocols catenate saturated hydrocarbons in a predictable manner. We report here the highly selective carbon-hydrogen (C-H) activation and subsequent dehydrogenative C-C coupling reaction of long-chain (>C(20)) linear alkanes on an anisotropic gold(110) surface, which undergoes an appropriate reconstruction by adsorption of the molecules and subsequent mild annealing, resulting in nanometer-sized channels (1.22 nanometers in width). Owing to the orientational constraint of the reactant molecules in these one-dimensional channels, the reaction takes place exclusively at specific sites (terminal CH(3) or penultimate CH(2) groups) in the chains at intermediate temperatures (420 to 470 kelvin) and selects for aliphatic over aromatic C-H activation.
Control of optical bistability and third-order nonlinearity via tunneling induced quantum interference in triangular quantum dot molecules

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

Tian, Si-Cong, E-mail: tiansicong@ciomp.ac.cn; Tong, Cun-Zhu, E-mail: tongcz@ciomp.ac.cn; Zhang, Jin-Long

The optical bistability of a triangular quantum dot molecules embedded inside a unidirectional ring cavity is studied. The type, the threshold and the hysteresis loop of the optical bistability curves can be modified by the tunneling parameters, as well as the probe laser field. The linear and nonlinear susceptibilities of the medium are also studied to interpret the corresponding results. The physical interpretation is that the tunneling can induce the quantum interference, which modifies the linear and the nonlinear response of the medium. As a consequence, the characteristics of the optical bistability are changed. The scheme proposed here can bemore » utilized for optimizing and controlling the optical switching process.« less
Site-specific recoil-induced effects on inner-shell photoionization of linear triatomic molecules: N 1 s photoelectron spectra of N2 O

NASA Astrophysics Data System (ADS)

Krivosenko, Yu. S.; Pavlychev, A. A.

2016-11-01

We investigate hard X-ray ionization of linear triatomic molecules accenting recoil-induced effects on the dynamics of molecular frame. This dynamics is studied within the two-springs and harmonic approximations. The mode-channel relationship connecting the excitations of vibrational, rotational and translational degrees of freedom with the Σ → Σ and Σ → Π photoionization channels is applied to compute the N 1s-1 photoelectron spectra of molecular N2 O for various photon energies. The distinct ionized-site- and molecular-orientation-specific changes in the vibration structure of the 1 s photoelectron lines of terminal and central nitrogen atoms are revealed and discussed.
Aerosol dilution as a simple strategy for analysis of complex samples by ICP-MS.

PubMed

Barros, Ariane I; Pinheiro, Fernanda C; Amaral, Clarice D B; Lorençatto, Rodolfo; Nóbrega, Joaquim A

2018-02-01

This study investigated the capability of High Matrix Introduction (HMI) strategy for analysis of dialysis solution and urine samples using inductively coupled plasma mass spectrometry. The use of HMI enables the direct introduction of urine samples and dialysis solutions 2-fold diluted with 0.14molL -1 HNO 3 . Bismuth, Ge, Ir, Li, Pt, Rh, Sc and Tl were evaluated as internal standards for Al, Ag, As, Be, Cd, Cr, Pb, Sb, Se, Tl, and Hg determination in dialysis solution and As, Cd, Hg and Pb determination in urine samples. Helium collision cell mode (4.5mLmin -1 ) was efficient to overcome polyatomic interferences in As, Se and Cr determinations. Mercury memory effects were evaluated by washing with 0.12molL -1 HCl or an alkaline diluent solution prepared with n-butanol, NH 4 OH, EDTA, and Triton X-100. This later solution was efficient for avoiding Hg memory effects in 6h of analysis. Linear calibration curves were obtained for all analytes and detection limits were lower than maximum amounts allowed by Brazilian legislations. Recoveries for all analytes in dialysis solutions and urine samples ranged from 82% to 125% and relative standard deviations for all elements and samples were lower than 7%. Analysis of control internal urine samples was in agreement with certified values at 95% confidence level (t-test; p < 0.05). Copyright © 2017 Elsevier B.V. All rights reserved.
Investigation of the linear and second-order nonlinear optical properties of molecular crystals within the local field theory.

PubMed

Seidler, Tomasz; Stadnicka, Katarzyna; Champagne, Benoît

2013-09-21

In this paper it is shown that modest calculations combining first principles evaluations of the molecular properties with electrostatic interaction schemes to account for the crystal environment effects are reliable for predicting and interpreting the experimentally measured electric linear and second-order nonlinear optical susceptibilities of molecular crystals within the experimental error bars. This is illustrated by considering two molecular crystals, namely: 2-methyl-4-nitroaniline and 4-(N,N-dimethylamino)-3-acetamidonitrobenzene. Three types of surrounding effects should be accounted for (i) the polarization due to the surrounding molecules, described here by static electric fields originating from their electric dipoles or charge distributions, (ii) the intermolecular interactions, which affect the geometry and particularly the molecular conformation, and (iii) the screening of the external electric field by the constitutive molecules. This study further highlights the role of electron correlation on the linear and nonlinear responses of molecular crystals and the challenge of describing frequency dispersion.
A structural diagnostics diagram for metallofullerenes encapsulating metal carbides and nitrides.

PubMed

Maki, Sachiko; Nishibori, Eiji; Terauchi, Ikuya; Ishihara, Masayuki; Aoyagi, Shinobu; Sakata, Makoto; Takata, Masaki; Umemoto, Hisashi; Inoue, Takashi; Shinohara, Hisanori

2013-01-16

Systematic structural studies of 24 different kinds of endohedral metallofullerenes, M(x)C(2n) (M = La, Y, Sc, Lu, Ti, Eu, Er, Hf, Sc(3)N; 34 ≤ n ≤ 43), as 1:1 cocrystals with solvent toluene molecules have been carried out using synchrotron radiation powder diffraction. Thirteen of the 24 molecular structures, including five metal carbides, one metal nitride endohedral fullerene, and one hollow fullerene, have been determined by a combination of the maximum entropy method and Rietveld refinement of the X-ray diffraction data obtained. We have found that the volume for one fullerene and one toluene molecule depends linearly on the number of carbon atoms in the fullerene cage. Fifteen different kinds of metal carbide endohedral fullerenes have been identified, which can be structurally characterized from the obtained lattice constants using only this linear dependence. The linear dependence found in the present study provides a metallofullerene diagnostics diagram that may have universal importance for structural characterization of the so-called cluster endohedral fullerenes.
Novel linear polymers able to inhibit bacterial quorum sensing.

PubMed

Cavaleiro, Eliana; Duarte, Ana Sofia; Esteves, Ana Cristina; Correia, António; Whitcombe, Michael J; Piletska, Elena V; Piletsky, Sergey A; Chianella, Iva

2015-05-01

Bacterial phenotypes, such as biofilm formation, antibiotic resistance and virulence expression, are associated with quorum sensing. Quorum sensing is a density-dependent regulatory system of gene expression controlled by specific signal molecules, such as N-acyl homoserine lactones (AHLs), produced and released by bacteria. This study reports the development of linear polymers capable to attenuate quorum sensing by adsorption of AHLs. Linear polymers were synthesized using MMA as backbone monomer and methacrylic acid and itaconic acid as functional monomers. Two different quorum sensing-controlled phenotypes, Vibrio fischeri bioluminescence and Aeromonas hydrophila biofilm formation, were evaluated to test the polymers' efficiency. Results showed that both phenotypes were significantly affected by the polymers, with the itaconic acid-containing material being more effective than the methacrylic acid one. The polymer inhibitory effects were reverted by the addition of lactones, confirming attenuation of quorum sensing through sequestration of signal molecules. The polymers also showed no cytotoxicity when tested using a mammalian cell line. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Comparison of gas-solid chromatography and MM2 force field molecular binding energies for greenhouse gases on a carbonaceous surface.

PubMed

Rybolt, Thomas R; Bivona, Kevin T; Thomas, Howard E; O'Dell, Casey M

2009-10-01

Gas-solid chromatography was used to determine B(2s) (gas-solid virial coefficient) values for eight molecular adsorbates interacting with a carbon powder (Carbopack B, Supelco). B(2s) values were determined by multiple size variant injections within the temperature range of 313-553 K. The molecular adsorbates included: carbon dioxide (CO(2)); tetrafluoromethane (CF(4)); hexafluoroethane (C(2)F(6)); 1,1-difluoroethane (C(2)H(4)F(2)); 1-chloro-1,1-difluoroethane (C(2)H(3)ClF(2)); dichlorodifluoromethane (CCl(2)F(2)); trichlorofluoromethane (CCl(3)F); and 1,1,1-trichloroethane (C(2)H(3)Cl(3)). Two of these molecules are of special interest because they are "super greenhouse gases". The global warming potential, GWP, for CF(4) is 6500 and for C(2)F(6) is 9200 relative to the reference value of 1 for CO(2). The GWP index considers both radiative blocking and molecular lifetime. For these and other industrial greenhouse gases, adsorptive trapping on a carbonaceous solid, which depends on molecule-surface binding energy, could avoid atmospheric release. The temperature variations of the gas-solid virial coefficients in conjunction with van't Hoff plots were used to find the experimental adsorption energy or binding energy values (E(*)) for each adsorbate. A molecular mechanics based, rough-surface model was used to calculate the molecule-surface binding energy (Ecal(*)) using augmented MM2 parameters. The surface model consisted of parallel graphene layers with two separated nanostructures each containing 17 benzene rings arranged in linear strips. The separation of the parallel nanostructures had been optimized in a prior study to appropriately represent molecule-surface interactions for Carbopack B. Linear regressions of E(*) versus Ecal(*) for the current data set of eight molecules and the same surface model gave E(*)=0.926 Ecal(*) and r(2)=0.956. A combined set of the current and prior Carbopack B adsorbates studied (linear alkanes, branched alkanes, cyclic alkanes, ethers, and halogenated hydrocarbons) gave a data set with 33 molecules and a regression of E(*)=0.991 Ecal(*) and r(2)=0.968. These results indicated a good correlation between the experimental and the MM2 computed molecule-surface binding energies.
An empirical model for ion formation from polymer surfaces during analysis by secondary ion mass spectrometry

NASA Astrophysics Data System (ADS)

Leggett, Graham J.; Vickerman, John C.

1992-12-01

Some of the models that have been proposed to account for ion formation during sputtering are reviewed. Particular attention is paid to models describing polyatomic ion formation. Aspects of these models that are relevant to ion formation from molecular materials are discussed. Reports describing the sputtering of polymeric materials are reviewed, and the bearing of recent tandem studies on attempts to formulate a model for ion formation from polymer materials is discussed. Some of the characteristics that a suitable model would possess are identified from the experimental data.
Radical chemistry of artemisinin

NASA Astrophysics Data System (ADS)

Denisov, Evgenii T.; Solodova, S. L.; Denisova, Taisa G.

2010-12-01

The review summarizes physicochemical characteristics of the natural sesquiterpene peroxide artemisinin. The kinetic schemes of transformations of artemisinin radicals under anaerobic conditions are presented and analyzed. The sequence of radical reactions of artemisinin in the presence of oxygen is considered in detail. Special emphasis is given to the intramolecular chain oxidation resulting in the transformation of artemisinin into polyatomic hydroperoxide. The kinetic characteristics of elementary reaction steps involving alkyl, alkoxyl, and peroxyl radicals generated from artemisinin are discussed. The results of testing of artemisinin and its derivatives for the antimalarial activity and the scheme of the biochemical synthesis of artemisinin in nature are considered.

Ultraviolet laser spectroscopy of jet-cooled CaNC and SrNC free radicals: Observation of bent excited electronic states

NASA Astrophysics Data System (ADS)

Greetham, Gregory M.; Ellis, Andrew M.

2000-11-01

New electronic transitions of the CaNC and SrNC free radicals have been identified in the near ultraviolet. For CaNC one new system, labeled the D˜-X˜ transition, was observed in the 31 500-33 400 cm-1 region. Two new transitions were found for SrNC, the D˜-X˜ and Ẽ-X˜ systems spanning 29 100-31 000 and 32 750-34 000 cm-1, respectively. Jet-cooled laser excitation spectra yield complex vibrational structure, much of which is attributed to excitation of the bending vibration. This has been used to infer that the molecule adopts a nonlinear equilibrium geometry in the upper electronic state in all three band systems, in contrast to the linear ground electronic state. This structural change is accounted for by the increased diffuseness of the unpaired electron in the excited states, which favors deviation from linearity. All three new excited states are assigned 2A' symmetry and correlate with 2Σ+ states in the linear molecule limit. Tentative estimates for the barriers to linearity in the D˜ 2A' states of CaNC and SrNC have been determined as ˜700 and ˜1050 cm-1, respectively.
Imaging fluorescence detected linear dichroism of plant cell walls in laser scanning confocal microscope.

PubMed

Steinbach, Gábor; Pomozi, István; Zsiros, Ottó; Páy, Anikó; Horváth, Gábor V; Garab, Gyozo

2008-03-01

Anisotropy carries important information on the molecular organization of biological samples. Its determination requires a combination of microscopy and polarization spectroscopy tools. The authors constructed differential polarization (DP) attachments to a laser scanning microscope in order to determine physical quantities related to the anisotropic distribution of molecules in microscopic samples; here the authors focus on fluorescence-detected linear dichroism (FDLD). By modulating the linear polarization of the laser beam between two orthogonally polarized states and by using a demodulation circuit, the authors determine the associated transmitted and fluorescence intensity-difference signals, which serve the basis for LD (linear dichroism) and FDLD, respectively. The authors demonstrate on sections of Convallaria majalis root tissue stained with Acridin Orange that while (nonconfocal) LD images remain smeared and weak, FDLD images recorded in confocal mode reveal strong anisotropy of the cell wall. FDLD imaging is suitable for mapping the anisotropic distribution of transition dipoles in 3 dimensions. A mathematical model is proposed to account for the fiber-laminate ultrastructure of the cell wall and for the intercalation of the dye molecules in complex, highly anisotropic architecture. Copyright 2007 International Society for Analytical Cytology.
Multivalency of Sonic hedgehog conjugated to linear polymer chains modulates protein potency.

PubMed

Wall, Samuel T; Saha, Krishanu; Ashton, Randolph S; Kam, Kimberly R; Schaffer, David V; Healy, Kevin E

2008-04-01

A potently active multivalent form of the protein Sonic hedgehog (Shh) was produced by bioconjugation of a modified recombinant form of Shh to the linear polymers poly(acrylic acid) (pAAc) and hyaluronic acid (HyA) via a two-step reaction exploiting carboimiide and maleimide chemistry. Efficiency of the conjugation was approximately 75% even at stoichiometric ratios of 30 Shh molecules per linear HyA chain (i.e., 30:1 Shh/HyA). Bioactivity of the conjugates was tested via a cellular assay across a range of stoichiometric ratios of Shh molecules to HyA linear chains, which was varied from 0.6:1 Shh/HyA to 22:1 Shh/HyA. Results indicate that low conjugation ratios decrease Shh bioactivity and high ratios increase this activity beyond the potency of monomeric Shh, with approximately equal activity between monomeric soluble Shh and conjugated Shh at 7:1 Shh/HyA. In addition, high-ratio constructs increased angiogenesis determined by the in vivo chick chorioallantoic membrane (CAM) assay. These results are captured by a kinetic model of multiple interactions between the Shh/HyA conjugates and cell surface receptors resulting in higher cell signaling at lower bulk Shh concentrations.
Gas-phase ion-molecule reactions for the identification of the sulfone functionality in protonated analytes in a linear quadrupole ion trap mass spectrometer.

PubMed

Tang, Weijuan; Sheng, Huaming; Kong, John Y; Yerabolu, Ravikiran; Zhu, Hanyu; Max, Joann; Zhang, Minli; Kenttämaa, Hilkka I

2016-06-30

The oxidation of sulfur atoms is an important biotransformation pathway for many sulfur-containing drugs. In order to rapidly identify the sulfone functionality in drug metabolites, a tandem mass spectrometric method based on ion-molecule reactions was developed. A phosphorus-containing reagent, trimethyl phosphite (TMP), was allowed to react with protonated analytes with various functionalities in a linear quadrupole ion trap mass spectrometer. The reaction products and reaction efficiencies were measured. Only protonated sulfone model compounds were found to react with TMP to form a characteristic [TMP adduct-MeOH] product ion. All other protonated compounds investigated, with functionalities such as sulfoxide, N-oxide, hydroxylamino, keto, carboxylic acid, and aliphatic and aromatic amino, only react with TMP via proton transfer and/or addition. The specificity of the reaction was further demonstrated by using a sulfoxide-containing anti-inflammatory drug, sulindac, as well as its metabolite sulindac sulfone. A method based on functional group-selective ion-molecule reactions in a linear quadrupole ion trap mass spectrometer has been demonstrated for the identification of the sulfone functionality in protonated analytes. A characteristic [TMP adduct-MeOH] product ion was only formed for the protonated sulfone analytes. The applicability of the TMP reagent in identifying sulfone functionalities in drug metabolites was also demonstrated. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.
The mitochondrial genome of Hydra oligactis (Cnidaria, Hydrozoa) sheds new light on animal mtDNA evolution and cnidarian phylogeny.

PubMed

Kayal, Ehsan; Lavrov, Dennis V

2008-02-29

The 16,314-nuceotide sequence of the linear mitochondrial DNA (mtDNA) molecule of Hydra oligactis (Cnidaria, Hydrozoa)--the first from the class Hydrozoa--has been determined. This sequence contains genes for 13 energy pathway proteins, small and large subunit rRNAs, and methionine and tryptophan tRNAs, as is typical for cnidarians. All genes have the same transcriptional orientation and their arrangement in the genome is similar to that of the jellyfish Aurelia aurita. In addition, a partial copy of cox1 is present at one end of the molecule in a transcriptional orientation opposite to the rest of the genes, forming a part of inverted terminal repeat characteristic of linear mtDNA and linear mitochondrial plasmids. The sequence close to at least one end of the molecule contains several homonucleotide runs as well as small inverted repeats that are able to form strong secondary structures and may be involved in mtDNA maintenance and expression. Phylogenetic analysis of mitochondrial genes of H. oligactis and other cnidarians supports the Medusozoa hypothesis but also suggests that Anthozoa may be paraphyletic, with octocorallians more closely related to the Medusozoa than to the Hexacorallia. The latter inference implies that Anthozoa is paraphyletic and that the polyp (rather than a medusa) is the ancestral body type in Cnidaria.
Autonomous replication and addition of telomerelike sequences to DNA microinjected into Paramecium tetraurelia macronuclei.

PubMed Central

Gilley, D; Preer, J R; Aufderheide, K J; Polisky, B

1988-01-01

Paramecium tetraurelia can be transformed by microinjection of cloned serotype A gene sequences into the macronucleus. Transformants are detected by their ability to express serotype A surface antigen from the injected templates. After injection, the DNA is converted from a supercoiled form to a linear form by cleavage at nonrandom sites. The linear form appears to replicate autonomously as a unit-length molecule and is present in transformants at high copy number. The injected DNA is further processed by the addition of paramecium-type telomeric sequences to the termini of the linear DNA. To examine the fate of injected linear DNA molecules, plasmid pSA14SB DNA containing the A gene was cleaved into two linear pieces, a 14-kilobase (kb) piece containing the A gene and flanking sequences and a 2.2-kb piece consisting of the procaryotic vector. In transformants expressing the A gene, we observed that two linear DNA species were present which correspond to the two species injected. Both species had Paramecium telomerelike sequences added to their termini. For the 2.2-kb DNA, we show that the site of addition of the telomerelike sequences is directly at one terminus and within one nucleotide of the other terminus. These results indicate that injected procaryotic DNA is capable of autonomous replication in Paramecium macronuclei and that telomeric addition in the macronucleus does not require specific recognition sequences. Images PMID:3211128
Construction of trypanosome artificial mini-chromosomes.

PubMed Central

Lee, M G; E, Y; Axelrod, N

1995-01-01

We report the preparation of two linear constructs which, when transformed into the procyclic form of Trypanosoma brucei, become stably inherited artificial mini-chromosomes. Both of the two constructs, one of 10 kb and the other of 13 kb, contain a T.brucei PARP promoter driving a chloramphenicol acetyltransferase (CAT) gene. In the 10 kb construct the CAT gene is followed by one hygromycin phosphotransferase (Hph) gene, and in the 13 kb construct the CAT gene is followed by three tandemly linked Hph genes. At each end of these linear molecules are telomere repeats and subtelomeric sequences. Electroporation of these linear DNA constructs into the procyclic form of T.brucei generated hygromycin-B resistant cell lines. In these cell lines, the input DNA remained linear and bounded by the telomere ends, but it increased in size. In the cell lines generated by the 10 kb construct, the input DNA increased in size to 20-50 kb. In the cell lines generated by the 13 kb constructs, two sizes of linear DNAs containing the input plasmid were detected: one of 40-50 kb and the other of 150 kb. The increase in size was not the result of in vivo tandem repetitions of the input plasmid, but represented the addition of new sequences. These Hph containing linear DNA molecules were maintained stably in cell lines for at least 20 generations in the absence of drug selection and were subsequently referred to as trypanosome artificial mini-chromosomes, or TACs. Images PMID:8532534
A simple model for electrical charge in globular macromolecules and linear polyelectrolytes in solution

NASA Astrophysics Data System (ADS)

Krishnan, M.

2017-05-01

We present a model for calculating the net and effective electrical charge of globular macromolecules and linear polyelectrolytes such as proteins and DNA, given the concentration of monovalent salt and pH in solution. The calculation is based on a numerical solution of the non-linear Poisson-Boltzmann equation using a finite element discretized continuum approach. The model simultaneously addresses the phenomena of charge regulation and renormalization, both of which underpin the electrostatics of biomolecules in solution. We show that while charge regulation addresses the true electrical charge of a molecule arising from the acid-base equilibria of its ionizable groups, charge renormalization finds relevance in the context of a molecule's interaction with another charged entity. Writing this electrostatic interaction free energy in terms of a local electrical potential, we obtain an "interaction charge" for the molecule which we demonstrate agrees closely with the "effective charge" discussed in charge renormalization and counterion-condensation theories. The predictions of this model agree well with direct high-precision measurements of effective electrical charge of polyelectrolytes such as nucleic acids and disordered proteins in solution, without tunable parameters. Including the effective interior dielectric constant for compactly folded molecules as a tunable parameter, the model captures measurements of effective charge as well as published trends of pKa shifts in globular proteins. Our results suggest a straightforward general framework to model electrostatics in biomolecules in solution. In offering a platform that directly links theory and experiment, these calculations could foster a systematic understanding of the interrelationship between molecular 3D structure and conformation, electrical charge and electrostatic interactions in solution. The model could find particular relevance in situations where molecular crystal structures are not available or rapid, reliable predictions are desired.
Further Analysis of Boiling Points of Small Molecules, CH[subscript w]F[subscript x]Cl[subscript y]Br[subscript z

ERIC Educational Resources Information Center

Beauchamp, Guy

2005-01-01

A study to present specific hypothesis that satisfactorily explain the boiling point of a number of molecules, CH[subscript w]F[subscript x]Cl[subscript y]Br[subscript z] having similar structure, and then analyze the model with the help of multiple linear regression (MLR), a data analysis tool. The MLR analysis was useful in selecting the…
Energy-switching potential energy surface for the water molecule revisited: A highly accurate singled-sheeted form.

PubMed

Galvão, B R L; Rodrigues, S P J; Varandas, A J C

2008-07-28

A global ab initio potential energy surface is proposed for the water molecule by energy-switching/merging a highly accurate isotope-dependent local potential function reported by Polyansky et al. [Science 299, 539 (2003)] with a global form of the many-body expansion type suitably adapted to account explicitly for the dynamical correlation and parametrized from extensive accurate multireference configuration interaction energies extrapolated to the complete basis set limit. The new function mimics also the complicated Sigma/Pi crossing that arises at linear geometries of the water molecule.
Non-detection of HC11N towards TMC-1: constraining the chemistry of large carbon-chain molecules

NASA Astrophysics Data System (ADS)

Loomis, Ryan A.; Shingledecker, Christopher N.; Langston, Glen; McGuire, Brett A.; Dollhopf, Niklaus M.; Burkhardt, Andrew M.; Corby, Joanna; Booth, Shawn T.; Carroll, P. Brandon; Turner, Barry; Remijan, Anthony J.

2016-12-01

Bell et al. reported the first detection of the cyanopolyyne HC11N towards the cold dark cloud TMC-1; no subsequent detections have been reported towards any source. Additional observations of cyanopolyynes and other carbon-chain molecules towards TMC-1 have shown a log-linear trend between molecule size and column density, and in an effort to further explore the underlying chemical processes driving this trend, we have analysed Green Bank Telescope observations of HC9N and HC11N towards TMC-1. Although we find an HC9N column density consistent with previous values, HC11N is not detected and we derive an upper limit column density significantly below that reported in Bell et al. Using a state-of-the-art chemical model, we have investigated possible explanations of non-linearity in the column density trend. Despite updating the chemical model to better account for ion-dipole interactions, we are not able to explain the non-detection of HC11N, and we interpret this as evidence of previously unknown carbon-chain chemistry. We propose that cyclization reactions may be responsible for the depleted HC11N abundance, and that products of these cyclization reactions should be investigated as candidate interstellar molecules.
Experimental Realization of Efficient, Room Temperature Single-Photon Sources with Definite Circular and Linear Polarizations

NASA Astrophysics Data System (ADS)

Boutsidis, Christos

In this thesis I present experimental demonstrations of room-temperature, single-photon sources with definite linear and circular polarizations. Definite photon polarization increases the efficiency of quantum communication systems. In contrast with cryogenic-temperature single-photon sources based on epitaxial quantum dots requiring expensive MBE and nanofabrication, my method utilizes a mature liquid crystal technology, which I made consistent with single-emitter fluorescence microscopy. The structures I have prepared are planar-aligned cholesteric liquid crystals forming 1-D photonic bandgaps for circularly-polarized light, which were used to achieve definite circularly-polarized fluorescence of single emitters doped in this environment. I also used planar-aligned nematic liquid crystals to align single molecules with linear dipole moments and achieved definite linearly-polarized fluorescence. I used single nanocrystal quantum dots, single nanodiamond color-centers, rare-earth-doped nanocrystals, and single terrylene and DiIC18(3) dye molecules as emitters. For nanocrystal quantum dots I observed circular polarization dissymmetry factors as large as ge = --1.6. In addition, I observed circularly-polarized resonances in the fluorescence of emitters within a cholesteric microcavity, with cavity quality factors of up to Q ˜ 250. I also showed that the fluorescence of DiIC18(3) dye molecules in planar-aligned nematic cells exhibits definite linear polarization, with a degree of polarization of rho = --0.58 +/- 0.03. Distributed Bragg reflectors form another type of microcavity that can be used to realize a single-photon source. I characterized the fluorescence from nanocrystal quantum dots doped in the defect layers of such microcavites, both organic and inorganic. Finally, to demonstrate the single-photon properties of single-emitter-doped cholesteric and nematic liquid crystal structures and distributed Bragg reflector microcavities, I present observations of photon antibunching from emitters doped in each of these structures. These experimental observations include photon antibunching from: nanocrystal quantum dots and nanodiamond color-centers doped in a cholesteric microcavity; terrylene and DiIC 18(3) dye molecules doped in nematic structures, and nanocrystal quantum dots doped in the distributed Bragg reflector microcavity. A value of the zero-time second-order coherence as low as g(2)(0) = 0.001 +/- 0.03 was measured. These results represent an important step forward in the realization of room temperature single-photon sources with definite polarization for secure quantum communication.
Application of the dressed-bound-state molecular strong-field approximation to above-threshold ionization of heteronuclear molecules: NO vs. CO.

PubMed

Busuladžić, M; Hasović, E; Becker, W; Milošević, D B

2012-10-07

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

PubMed

Keller, Andreas; Gerkin, Richard C; Guan, Yuanfang; Dhurandhar, Amit; Turu, Gabor; Szalai, Bence; Mainland, Joel D; Ihara, Yusuke; Yu, Chung Wen; Wolfinger, Russ; Vens, Celine; Schietgat, Leander; De Grave, Kurt; Norel, Raquel; Stolovitzky, Gustavo; Cecchi, Guillermo A; Vosshall, Leslie B; Meyer, Pablo

2017-02-24

It is still not possible to predict whether a given molecule will have a perceived odor or what olfactory percept it will produce. We therefore organized the crowd-sourced DREAM Olfaction Prediction Challenge. Using a large olfactory psychophysical data set, teams developed machine-learning algorithms to predict sensory attributes of molecules based on their chemoinformatic features. The resulting models accurately predicted odor intensity and pleasantness and also successfully predicted 8 among 19 rated semantic descriptors ("garlic," "fish," "sweet," "fruit," "burnt," "spices," "flower," and "sour"). Regularized linear models performed nearly as well as random forest-based ones, with a predictive accuracy that closely approaches a key theoretical limit. These models help to predict the perceptual qualities of virtually any molecule with high accuracy and also reverse-engineer the smell of a molecule. Copyright © 2017, American Association for the Advancement of Science.
Testing a new analytical approach for determination of vibrational transition moment directions in low symmetry planar molecules: 1-D- and 2-D-naphthalene.

PubMed

Rogojerov, Marin; Keresztury, Gábor; Kamenova-Nacheva, Mariana; Sundius, Tom

2012-12-01

A new analytical approach for improving the precision in determination of vibrational transition moment directions of low symmetry molecules (lacking orthogonal axes) is discussed in this paper. The target molecules are partially uniaxially oriented in nematic liquid crystalline solvent and are studied by IR absorption spectroscopy using polarized light. The fundamental problem addressed is that IR linear dichroism measurements of low symmetry molecules alone cannot provide sufficient information on molecular orientation and transition moment directions. It is shown that computational prediction of these quantities can supply relevant complementary data, helping to reveal the hidden information content and achieve a more meaningful and more precise interpretation of the measured dichroic ratios. The combined experimental and theoretical/computational method proposed by us recently for determination of the average orientation of molecules with C(s) symmetry has now been replaced by a more precise analytical approach. The new method introduced and discussed in full detail here uses a mathematically evaluated angle between two vibrational transition moment vectors as a reference. The discussion also deals with error analysis and estimation of uncertainties of the orientational parameters. The proposed procedure has been tested in an analysis of the infrared linear dichroism (IR-LD) spectra of 1-D- and 2-D-naphthalene complemented with DFT calculations using the scaled quantum mechanical force field (SQM FF) method. Copyright © 2012 Elsevier B.V. All rights reserved.
Enhancement of ultracold molecule formation by local control in the nanosecond regime

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

Carini, J. L.; Kallush, S.; Kosloff, R.

2015-02-01

We describe quantum simulations of ultracold 87Rb 2 molecule formation using photoassociation (PA) with nanosecond-time-scale pulses of frequency chirped light. In particular, we compare the case of a linear chirp to one where the frequency evolution is optimized by local control (LC) of the phase, and find that LC can provide a significant enhancement. The resulting optimal frequency evolution corresponds to a rapid jump from the PA absorption resonance to a downward transition to a bound level of the lowest triplet state. We also consider the case of two frequencies and investigate interference effects. The assumed chirp parameters should bemore » achievable with nanosecond pulse shaping techniques and are predicted to provide a significant enhancement over recent experiments with linear chirps.« less
Towards a universal method for calculating hydration free energies: a 3D reference interaction site model with partial molar volume correction.

PubMed

Palmer, David S; Frolov, Andrey I; Ratkova, Ekaterina L; Fedorov, Maxim V

2010-12-15

We report a simple universal method to systematically improve the accuracy of hydration free energies calculated using an integral equation theory of molecular liquids, the 3D reference interaction site model. A strong linear correlation is observed between the difference of the experimental and (uncorrected) calculated hydration free energies and the calculated partial molar volume for a data set of 185 neutral organic molecules from different chemical classes. By using the partial molar volume as a linear empirical correction to the calculated hydration free energy, we obtain predictions of hydration free energies in excellent agreement with experiment (R = 0.94, σ = 0.99 kcal mol (- 1) for a test set of 120 organic molecules).
Method for determining surface properties of microparticles

DOEpatents

Eisenthal, Kenneth B.

2000-01-01

Second harmonic generation (SHG), sum frequency generation (SFG) and difference frequency generation (DFG) can be used for surface analysis or characterization of microparticles having a non-metallic surface feature. The microparticles can be centrosymmetric or such that non-metallic molecules of interest are centrosymmetrically distributed inside and outside the microparticles but not at the surface of the microparticles where the asymmetry aligns the molecules. The signal is quadratic in incident laser intensity or proportional to the product of two incident laser intensities for SFG, it is sharply peaked at the second harmonic wavelength, quadratic in the density of molecules adsorbed onto the microparticle surface, and linear in microparticles density. In medical or pharmacological applications, molecules of interest may be of drugs or toxins, for example.
Symmetry of Carrier-Envelope Phase Difference Effects in Strong-Field, Few-Cycle Ionization of Atoms and Molecules

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

Martiny, Christian Per Juul; Madsen, Lars Bojer

2006-09-01

In few-cycle pulses, the exact value of the carrier-envelope phase difference (CEPD) has a pronounced influence on the ionization dynamics of atoms and molecules. We show that, for atoms in circularly polarized light, a change in the CEPD is mapped uniquely to an overall rotation of the system, and results for arbitrary CEPD are obtained by rotation of the results from a single calculation with fixed CEPD. For molecules, this is true only for linear molecules aligned parallel with the propagation direction of the field. The effects of CEPD are classified as geometric or nongeometric. The observations are exemplified bymore » strong-field calculations on hydrogen.« less
Controlling drug efficiency by encapsulation into carbon nanotubes: A theoretical study of the antitumor Cisplatin and the anti-HIV TIBO molecules

NASA Astrophysics Data System (ADS)

Bessrour, R.; Belmiloud, Y.; Hosni, Z.; Tangour, B.

2012-06-01

From the beginning of last century, Paul Ehrlich, a specialist in the immune system and the Nobel Prize (1908) had raised the possibility of "magic bullets" can directly address, in an organism, drugs in a particular area of the body, sparing all other parts of side effects. Carbon nanotubes (CNTs) have particular property to cross cell membranes easily. In an effort to optimize the use of CNT as drug nanocarriers, we divided our study into two parts. In the first, our concern was to find the minimum diameter of a single wall CNT can encapsulate an anticancer drug that iscisplatin without altering its geometry in order conserve its therapeutic power. Behavior of one and two Cisplatin(Cp) molecules confined in capped and opened single-walled carbon nanotubes (CNTs) is studied by means of ab-initio calculations. Single molecule binding energies clearly exhibit encapsulation dependence on tube diameters that range from 6.26 Å to 12.04 Å. A weak stabilization energy of the Cp@(11,0) equal to -70 kcal.mol-1 has been obtained corresponding to a CNT's diameter of 8.5Å. We noticed that Cisplatin molecule changes shape when encapsulated into CNTs' whose diameters are less than 7.6 Å. In the presence of a second Cisplatin molecule in the (10,0) CNT, preferred position stays parallel to CNT's axis leading to a linear density of roughly 1588 molecules/μm of CNT's length corresponding to a linear density of 7.9 10-19 g/μm. The 195Pt chemical shift tensors are calculated using GIAO method. NMR calculations reveal that Platinum chemical shift is sensitive to CNT's diameter and is linearly correlated to confinement energy. 195Pt chemical shift measurement may be a direct method to access to the diameter of the encapsulating CNT's and to control the amount of drug molecule transported by this CNT. In the second part, the opposite has been sought is to say how the use of nanotubes with different diameters can control the change in a geometry of an anti-HIV drug that is TIBO molecule to bypass the mutation of the virus which wiped out its therapeutic effect. This work deals with the butterfly conformation control of the anti-HIV TIBO molecule confined into carbon nanotubes (CNT). This theoretical study concerns the variation of some pertinent conformation descriptors such as butterfly angle, wingspan, volume, dipole moment, solvation energy and confinement energy versus carbon nanotube diameters. Obtained results show that it is possible to describe the configurations of actual drugs as 8-Cl or 9-Cl TIBO as the parent molecule TIBO encapsulated in an adequate CNT. Our approach indicates that drug confinement inside CNTs may be a promising way to use a same drug in order to fellow HIV virus mutations.

Linear- and angular-shaped naphthodithiophenes: selective synthesis, properties, and application to organic field-effect transistors.

PubMed

Shinamura, Shoji; Osaka, Itaru; Miyazaki, Eigo; Nakao, Akiko; Yamagishi, Masakazu; Takeya, Jun; Takimiya, Kazuo

2011-04-06

A straightforward synthetic approach that exploits linear- and angular-shaped naphthodithiophenes (NDTs) being potential as new core structures for organic semiconductors is described. The newly established synthetic procedure involves two important steps; one is the chemoselective Sonogashira coupling reaction on the trifluoromethanesulfonyloxy site over the bromine site enabling selective formation of o-bromoethynylbenzene substructures on the naphthalene core, and the other is a facile ring closing reaction of fused-thiophene rings from the o-bromoethynylbenzene substructures. As a result, three isomeric NDTs, naphtho[2,3-b:6,7-b']dithiophene, naphtho[2,3-b:7,6-b']dithiophenes, and naphtho[2,1-b:6,5-b']dithiophene, are selectively synthesized. Electrochemical and optical measurements of the parent NDTs indicated that the shape of the molecules plays an important role in determining the electronic structure of the compounds; the linear-shaped NDTs formally isoelectronic with naphthacene have lower oxidation potentials and more red-shifted absorption bands than those of the angular-shaped NDTs isoelectronic with chrysene. On the contrary, the performance of the thin-film-based field-effect transistors (FETs) using the dioctyl or diphenyl derivatives were much influenced by the symmetry of the molecules; centrosymmetric derivatives tend to give higher mobility (up to 1.5 cm(2) V(-1) s(-1)) than axisymmetric ones (∼0.06 cm(2) V(-1) s(-1)), implying that the intermolecular orbital overlap in the solid state is influenced by the symmetry of the molecules. These results indicate that the present NDT cores, in particular the linear-shaped, centrosymmetric naphtho[2,3-b:6,7-b']dithiophene, are promising building blocks for the development of organic semiconducting materials. © 2011 American Chemical Society
An Evaluation of Unit and ½ Mass Correction Approaches as a ...

EPA Pesticide Factsheets

Rare earth elements (REE) and certain alkaline earths can produce M+2 interferences in ICP-MS because they have sufficiently low second ionization energies. Four REEs (150Sm, 150Nd, 156Gd and 156Dy) produce false positives on 75As and 78Se and 132Ba can produce a false positive on 66Zn. Currently, US EPA Method 200.8 does not address these as sources of false positives. Additionally, these M+2 false positives are typically enhanced if collision cell technology is utilized to reduce polyatomic interferences associated with ICP-MS detection. Correction equations can be formulated using either a unit or ½ mass approach. The ½ mass correction approach does not suffer from the bias generated from polyatomic or end user based contamination at the unit mass but is limited by the abundance sensitivity of the adjacent mass. For instance, the use of m/z 78 in a unit mass correction of 156Gd on m/z 78 can be biased by residual 40Ar38Ar and 78Se while the ½ mass approach can use 77.5 or 78.5 and is limited by the abundance sensitivity issues from mass 77 and 78 or 78 and 79, respectively. This presentation will evaluate the use of both unit and ½ mass correction approaches as a means of addressing M+2 false positives within the context of updating US EPA Method 200.8. This evaluation will include the analysis of As and Se standards near the detection limit in the presence of low (2ppb) and high (50ppb) levels of REE with benchmark concentrations estimated using
High resolution ID-ICP-MS certification of an estuary water reference material (LGC 6016) and analysis of matrix induced polyatomic interferences.

PubMed

Evans, P; Fairman, B

2001-10-01

Reliable trace metal analysis of environmental samples is dependent upon the availability of high accuracy, matrix reference standards. Here, we present Cd, Cu, Ni, Pb and Zn isotope dilution determination for an estuary water certified reference material (LGC 6016). This work highlights the need for high-accuracy techniques in the development of trace element CRMs rather than conventional inter-laboratory trials. Certification of the estuary water LGC6016 was initially determined from a consensus mean from 14 laboratories but this was found to be unsatisfactory due to the large discrepancies in the reported concentrations. The material was re-analysed using isotope dilution ICP-MS techniques. Pb and Cd were determined using a conventional quadrupole ICP-MS (Elan 5000). Cu, Zn and Ni were determined using a magnetic sector ICP-MS (Finnigan Element), which allowed significant polyatomic interferences to be overcome. Using the magnetic sector instrument, precise mass calibration to within 0.02 amu permitted identification of the interferences. Most interferences derived from the sample matrix. For example, the high Na content causes interferences on 63Cu, due to the formation of 40Ar23Na and 23Na2 16O1H, which in a conventional quadrupole instrument would relate to an erroneous increase in signal intensity by up to 20%. For each analyte a combined uncertainty calculation was performed following the Eurachem/GTAC and ISO guideline. For each element a combined uncertainty of 2-3% was found, which represents a 10-fold improvement compared to certification by inter-laboratory comparison. Analysis of the combined uncertainty budget indicates that the majority of systematic uncertainty derives from the instrumental isotope ratio measurements.
Circular RNA: New Regulatory Molecules.

PubMed

Belousova, E A; Filipenko, M L; Kushlinskii, N E

2018-04-01

Circular RNA are a family of covalently closed circular RNA molecules, formed from pre-mRNA of coding genes by means of splicing (canonical and alternative noncanonical splicing). Maturation of circular RNA is regulated by cis- and trans-elements. Complete list of biological functions of these RNA is not yet compiled; however, their capacity to interact with specific microRNA and play a role of a depot attracts the greatest interest. This property makes circular RNA active regulatory transcription factors. Circular RNA have many advantages over their linear analogs: synthesis of these molecules is conservative, they are universal, characterized by clearly determined specificity, and are resistant to exonucleases. In addition, the level of their expression is often higher than that of their linear forms. It should be noted that expression of circular RNA is tissue-specific. Moreover, some correlations between changes in the repertoire and intensity of expression of circular RNA and the development of some pathologies have been detected. Circular RNA have certain advantages and can serve as new biomarkers for the diagnosis, prognosis, and evaluation of response to therapy.
Dynamical discrete/continuum linear response shells theory of solvation: convergence test for NH4+ and OH- ions in water solution using DFT and DFTB methods.

PubMed

de Lima, Guilherme Ferreira; Duarte, Hélio Anderson; Pliego, Josefredo R

2010-12-09

A new dynamical discrete/continuum solvation model was tested for NH(4)(+) and OH(-) ions in water solvent. The method is similar to continuum solvation models in a sense that the linear response approximation is used. However, different from pure continuum models, explicit solvent molecules are included in the inner shell, which allows adequate treatment of specific solute-solvent interactions present in the first solvation shell, the main drawback of continuum models. Molecular dynamics calculations coupled with SCC-DFTB method are used to generate the configurations of the solute in a box with 64 water molecules, while the interaction energies are calculated at the DFT level. We have tested the convergence of the method using a variable number of explicit water molecules and it was found that even a small number of waters (as low as 14) are able to produce converged values. Our results also point out that the Born model, often used for long-range correction, is not reliable and our method should be applied for more accurate calculations.
An accurate and linear-scaling method for calculating charge-transfer excitation energies and diabatic couplings

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

Pavanello, Michele; Van Voorhis, Troy; Visscher, Lucas

2013-02-07

Quantum-mechanical methods that are both computationally fast and accurate are not yet available for electronic excitations having charge transfer character. In this work, we present a significant step forward towards this goal for those charge transfer excitations that take place between non-covalently bound molecules. In particular, we present a method that scales linearly with the number of non-covalently bound molecules in the system and is based on a two-pronged approach: The molecular electronic structure of broken-symmetry charge-localized states is obtained with the frozen density embedding formulation of subsystem density-functional theory; subsequently, in a post-SCF calculation, the full-electron Hamiltonian and overlapmore » matrix elements among the charge-localized states are evaluated with an algorithm which takes full advantage of the subsystem DFT density partitioning technique. The method is benchmarked against coupled-cluster calculations and achieves chemical accuracy for the systems considered for intermolecular separations ranging from hydrogen-bond distances to tens of Angstroms. Numerical examples are provided for molecular clusters comprised of up to 56 non-covalently bound molecules.« less
An accurate and linear-scaling method for calculating charge-transfer excitation energies and diabatic couplings.

PubMed

Pavanello, Michele; Van Voorhis, Troy; Visscher, Lucas; Neugebauer, Johannes

2013-02-07

Quantum-mechanical methods that are both computationally fast and accurate are not yet available for electronic excitations having charge transfer character. In this work, we present a significant step forward towards this goal for those charge transfer excitations that take place between non-covalently bound molecules. In particular, we present a method that scales linearly with the number of non-covalently bound molecules in the system and is based on a two-pronged approach: The molecular electronic structure of broken-symmetry charge-localized states is obtained with the frozen density embedding formulation of subsystem density-functional theory; subsequently, in a post-SCF calculation, the full-electron Hamiltonian and overlap matrix elements among the charge-localized states are evaluated with an algorithm which takes full advantage of the subsystem DFT density partitioning technique. The method is benchmarked against coupled-cluster calculations and achieves chemical accuracy for the systems considered for intermolecular separations ranging from hydrogen-bond distances to tens of Ångstroms. Numerical examples are provided for molecular clusters comprised of up to 56 non-covalently bound molecules.
FAST TRACK COMMUNICATION: Conformation dependence of molecular conductance: chemistry versus geometry

NASA Astrophysics Data System (ADS)

Finch, Christopher M.; Sirichantaropass, Skon; Bailey, Steven W.; Grace, Iain M.; García-Suárez, Víctor M.; Lambert, Colin J.

2008-01-01

Recent experiments by Venkataraman et al (2006 Nature 442 904) on a series of molecular wires with varying chemical compositions revealed a linear dependence of the conductance on cos2 θ, where θ is the angle of twist between neighbouring aromatic rings. To investigate whether or not this dependence has a more general applicability, we present a first-principles theoretical study of the transport properties of this family of molecules as a function of the chemical composition, conformation and the contact atom and geometry. If the Fermi energy EF lies within the HOMO-LUMO (highest occupied molecular orbital-lowest unoccupied molecular orbital) gap, then we reproduce the above experimental results. More generally, however, if EF is located within either the LUMO or the HOMO states, the presence of resonances destroys the linear dependence of the conductance on cos2 θ and gives rise to non-monotonic behaviour associated with the level structure of the different molecules. Our results suggest that the above experiments provide a novel method for extracting spectroscopic information about molecules contacted to electrodes.
The inherent dynamics of a molecular liquid: geodesic pathways through the potential energy landscape of a liquid of linear molecules.

PubMed

Jacobson, Daniel; Stratt, Richard M

2014-05-07

Because the geodesic pathways that a liquid follows through its potential energy landscape govern its slow, diffusive motion, we suggest that these pathways are logical candidates for the title of a liquid's "inherent dynamics." Like their namesake "inherent structures," these objects are simply features of the system's potential energy surface and thus provide views of the system's structural evolution unobstructed by thermal kinetic energy. This paper shows how these geodesic pathways can be computed for a liquid of linear molecules, allowing us to see precisely how such molecular liquids mix rotational and translational degrees of freedom into their dynamics. The ratio of translational to rotational components of the geodesic path lengths, for example, is significantly larger than would be expected on equipartition grounds, with a value that scales with the molecular aspect ratio. These and other features of the geodesics are consistent with a picture in which molecular reorientation adiabatically follows translation-molecules largely thread their way through narrow channels available in the potential energy landscape.
The inherent dynamics of a molecular liquid: Geodesic pathways through the potential energy landscape of a liquid of linear molecules

NASA Astrophysics Data System (ADS)

Jacobson, Daniel; Stratt, Richard M.

2014-05-01

Because the geodesic pathways that a liquid follows through its potential energy landscape govern its slow, diffusive motion, we suggest that these pathways are logical candidates for the title of a liquid's "inherent dynamics." Like their namesake "inherent structures," these objects are simply features of the system's potential energy surface and thus provide views of the system's structural evolution unobstructed by thermal kinetic energy. This paper shows how these geodesic pathways can be computed for a liquid of linear molecules, allowing us to see precisely how such molecular liquids mix rotational and translational degrees of freedom into their dynamics. The ratio of translational to rotational components of the geodesic path lengths, for example, is significantly larger than would be expected on equipartition grounds, with a value that scales with the molecular aspect ratio. These and other features of the geodesics are consistent with a picture in which molecular reorientation adiabatically follows translation—molecules largely thread their way through narrow channels available in the potential energy landscape.
Anharmonic Infrared Spectroscopy through the Fourier Transform of Time Correlation Function Formalism in ONETEP.

PubMed

Vitale, Valerio; Dziedzic, Jacek; Dubois, Simon M-M; Fangohr, Hans; Skylaris, Chris-Kriton

2015-07-14

Density functional theory molecular dynamics (DFT-MD) provides an efficient framework for accurately computing several types of spectra. The major benefit of DFT-MD approaches lies in the ability to naturally take into account the effects of temperature and anharmonicity, without having to introduce any ad hoc or a posteriori corrections. Consequently, computational spectroscopy based on DFT-MD approaches plays a pivotal role in the understanding and assignment of experimental peaks and bands at finite temperature, particularly in the case of floppy molecules. Linear-scaling DFT methods can be used to study large and complex systems, such as peptides, DNA strands, amorphous solids, and molecules in solution. Here, we present the implementation of DFT-MD IR spectroscopy in the ONETEP linear-scaling code. In addition, two methods for partitioning the dipole moment within the ONETEP framework are presented. Dipole moment partitioning allows us to compute spectra of molecules in solution, which fully include the effects of the solvent, while at the same time removing the solvent contribution from the spectra.
Adsorption of polar organic molecules on sediments: Case-study on Callovian-Oxfordian claystone.

PubMed

Rasamimanana, S; Lefèvre, G; Dagnelie, R V H

2017-08-01

The release and transport of anthropogenic organic matter through the geosphere is often an environmental criterion of safety. Sedimentary rocks are widely studied in this context as geological barriers for waste management. It is the case of Callovian-Oxfordian claystone (COx), for which several studies report adsorption of anthropogenic organic molecules. In this study, we evaluated and reviewed adsorption data of polar organic molecules on COx claystone. Experiments were performed on raw claystone, decarbonated and clay fractions. Adsorption isotherms were measured with adsorbates of various polarities: adipate, benzoate, ortho-phthalate, succinate, gluconate, oxalate, EDTA, citrate. A significant adsorption was observed for multidentate polycarboxylic acids as evidenced with phthalate, succinate, oxalate, gluconate, EDTA and citrate (R d = 1.53, 3.52, 8.4, 8.8, 12.4, 54.7 L kg -1 respectively). Multiple linear regression were performed as a statistical analysis to determine the predictors from these adsorption data. A linear correlation between adsorption data (R d ) and dipole moment (μ) of adsorbates was evidenced (R 2 = 0.91). Molecules with a high dipole moment, μ(D) > 2.5, displayed a significant adsorption, R d ≫1 L kg -1 . A qualitative correlation can be easily estimated using the water/octanol partition coefficient, P ow , of adsorbates (R 2 = 0.77). In this case, two opposite trends were distinguished for polar and apolar molecules. The use of organic carbon content in sediments is relevant for predicting adsorption of apolar compounds, log (P ow )>+1. The oxides/clays contents may be relevant regarding polar molecules, log ( apparent P ow )<-1. The proposed scheme offers a general methodology for investigation of geo-barriers towards heterogeneous organic plumes. Copyright © 2017 Elsevier Ltd. All rights reserved.
Light-induced noncentrosymmetry in acceptor-donor-substituted azobenzene solutions

NASA Astrophysics Data System (ADS)

Zhao, Jiang; Si, Jinhai; Wang, Yougui; Ye, Peixian; Fu, Xingfa; Qiu, Ling; Shen, Yuquan

1995-10-01

Light-induced noncentrosymmetry was achieved experimentally in acceptor-donor-substituted azobenzene solutions and observed by phase-matched nondegenerate six-wave mixing. The microscopic origin of the induced noncentrosymmetry was found to be orientational hole burning, which was distinguished directly with net orientation of molecules by experimental observations. The decay time of the induced noncentrosymmetry depended on the rotational orientation time of the sample's molecule, which varied linearly with the viscosity of the solvent.
PCR-based detection of a rare linear DNA in cell culture.

PubMed

Saveliev, Sergei V.

2002-11-11

The described method allows for detection of rare linear DNA fragments generated during genomic deletions. The predicted limit of the detection is one DNA molecule per 10(7) or more cells. The method is based on anchor PCR and involves gel separation of the linear DNA fragment and chromosomal DNA before amplification. The detailed chemical structure of the ends of the linear DNA can be defined with the use of additional PCR-based protocols. The method was applied to study the short-lived linear DNA generated during programmed genomic deletions in a ciliate. It can be useful in studies of spontaneous DNA deletions in cell culture or for tracking intracellular modifications at the ends of transfected DNA during gene therapy trials.
PCR-based detection of a rare linear DNA in cell culture

PubMed Central

2002-01-01

The described method allows for detection of rare linear DNA fragments generated during genomic deletions. The predicted limit of the detection is one DNA molecule per 107 or more cells. The method is based on anchor PCR and involves gel separation of the linear DNA fragment and chromosomal DNA before amplification. The detailed chemical structure of the ends of the linear DNA can be defined with the use of additional PCR-based protocols. The method was applied to study the short-lived linear DNA generated during programmed genomic deletions in a ciliate. It can be useful in studies of spontaneous DNA deletions in cell culture or for tracking intracellular modifications at the ends of transfected DNA during gene therapy trials. PMID:12734566
Vibrational spectroscopic and non-linear optical activity studies on nicotinanilide : A DFT approach

NASA Astrophysics Data System (ADS)

Premkumar, S.; Jawahar, A.; Mathavan, T.; Dhas, M. Kumara; Benial, A. Milton Franklin

2015-06-01

The molecular structure of nicotinanilide was optimized by the DFT/B3LYP method with cc-pVTZ basis set using Gaussian 09 program. The first order hyperpolarizability of the molecule was calculated, which exhibits the higher nonlinear optical activity. The natural bond orbital analysis confirms the presence of intramolecular charge transfer and the hydrogen bonding interaction, which leads to the higher nonlinear optical activity of the molecule. The Frontier molecular orbitals analysis of the molecule shows that the delocalization of electron density occurs within the molecule. The lower energy gap indicates that the hydrogen bond formation between the charged species. The vibrational frequencies were calculated and assigned on the basis of potential energy distribution calculation using the VEDA 4.0 program and the corresponding vibrational spectra were simulated. Hence, the nicotinanilide molecule can be a good candidate for second-order NLO material.
Interaction between perylene-derivated molecules observed by low temperature scanning tunneling microscopy

NASA Astrophysics Data System (ADS)

Vernisse, Loranne; Guillermet, Olivier; Gourdon, André; Coratger, Roland

2018-03-01

Derivative perylene molecules deposited on Ag(111) and on NaCl(001) ultrathin layers have been investigated using low temperature STM and NC-AFM. When the metallic substrate is held at ambient temperature during evaporation, the molecules form characteristic trimers on the Ag(111) surface and interact through their polar groups. Close to the steps, the molecules form linear structures and seems to stand side by side. On the other hand, after deposition on a substrate cooled at liquid helium temperature, single molecules are observed both on metal and on NaCl. On the ultrathin insulator layers, the STM images present characteristic contrasts related to the molecular orbitals which favors the localization of aldehyde groups. In this case, the lateral molecular interactions may induce the formation of small assemblies in which the electronic levels are slightly shifted. A possible interpretation of this phenomenon is to take into account polar interactions and charge transfer between neighboring molecules.
Viscous properties of isotropic fluids composed of linear molecules: departure from the classical Navier-Stokes theory in nano-confined geometries.

PubMed

Hansen, J S; Daivis, Peter J; Todd, B D

2009-10-01

In this paper we present equilibrium molecular-dynamics results for the shear, rotational, and spin viscosities for fluids composed of linear molecules. The density dependence of the shear viscosity follows a stretched exponential function, whereas the rotational viscosity and the spin viscosities show approximately power-law dependencies. The frequency-dependent shear and spin viscosities are also studied. It is found that viscoelastic behavior is first manifested in the shear viscosity and that the real part of the spin viscosities features a maximum for nonzero frequency. The calculated transport coefficients are used together with the extended Navier-Stokes equations to investigate the effect of the coupling between the intrinsic angular momentum and linear momentum for highly confined fluids. Both steady and oscillatory flows are studied. It is shown, for example, that the fluid flow rate for Poiseuille flow is reduced by up to 10% in a 2 nm channel for a buta-triene fluid at density 236 kg m(-3) and temperature 306 K. The coupling effect may, therefore, become very important for nanofluidic applications.
Spectroscopic investigations using density functional theory on 2-methoxy- 4(phenyliminomethyl)phenol: A non linear optical material

NASA Astrophysics Data System (ADS)

Hijas, K. M.; Madan Kumar, S.; Byrappa, K.; Geethakrishnan, T.; Jeyaram, S.; Nagalakshmi, R.

2018-03-01

Single crystals of 2-methoxy-4(phenyliminomethyl)phenol were grown from ethanol by slow evaporation solution growth technique. Single crystal X-ray diffraction experiment reveals the crystallization in orthorhombic system having non-centrosymmetric space group C2221. Geometrical optimization by density functional theory method was carried out using Gaussian program and compared with experimental results. Detailed experimental and theoretical vibrational analyses were carried out and the results were correlated to find close agreement. Thermal analyses show the material is thermally stable with a melting point of 159 °C. Natural bond orbital analysis was carried out to explain charge transfer interactions through hydrogen bonding. Relatively smaller HOMO-LUMO band gap favors the non linear optical activity of the molecule. Natural population analysis and molecular electrostatic potential calculations visualize the charge distribution in an isolated molecule. Calculated first-order molecular hyperpolarizability and preliminary second harmonic generation test carried out using Kurtz-Perry technique establish 2-methoxy-4(phenyliminomethyl)phenol crystal as a good non linear optical material. Z-scan proposes the material for reverse saturable absorption.
Structure of Irreversibly Adsorbed Star Polymers

NASA Astrophysics Data System (ADS)

Akgun, Bulent; Aykan, Meryem Seyma; Canavar, Seda; Satija, Sushil K.; Uhrig, David; Hong, Kunlun

Formation of irreversibly adsorbed polymer chains on solid substrates have a huge impact on the wetting, glass transition, aging and polymer chain mobility in thin films. In recent years there has been many reports on the formation, kinetics and dynamics of these layers formed by linear homopolymers. Recent studies showed that by varying the number of polymer arms and arm molecular weight one can tune the glass transition temperature of thin polymer films. Using polymer architecture as a tool, the behavior of thin films can be tuned between the behavior of linear chains and soft colloids. We have studied the effect of polymer chain architecture on the structure of dead layer using X-ray reflectivity (XR) and atomic force microscopy. Layer thicknesses and densities of flattened and loosely adsorbed chains has been measured for linear, 4-arm, and 8-arm star polymers with identical total molecular weight as a function of substrate surface energy, annealing temperature and annealing time. Star polymers have been synthesized using anionic polymerization. XR measurements showed that 8-arm star PS molecules form the densest and the thickest dead layers among these three molecules.

Valence electronic properties of porphyrin derivatives.

PubMed

Stenuit, G; Castellarin-Cudia, C; Plekan, O; Feyer, V; Prince, K C; Goldoni, A; Umari, P

2010-09-28

We present a combined experimental and theoretical investigation of the valence electronic structure of porphyrin-derived molecules. The valence photoemission spectra of the free-base tetraphenylporphyrin and of the octaethylporphyrin molecule were measured using synchrotron radiation and compared with theoretical spectra calculated using the GW method and the density-functional method within the generalized gradient approximation. Only the GW results could reproduce the experimental data. We found that the contribution to the orbital energies due to electronic correlations has the same linear behavior in both molecules, with larger deviations in the vicinity of the HOMO level. This shows the importance of adequate treatment of electronic correlations in these organic systems.
Global bending quantum number and the absence of monodromy in the HCN{r_reversible}CNH molecule

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

Efstathiou, K.; Sadovskii, D.A.; Joyeux, M.

We introduce and analyze a model system based on a deformation of a spherical pendulum that can be used to reproduce large amplitude bending vibrations of flexible triatomic molecules with two stable linear equilibria. On the basis of our model and the recent vibrational potential [ J. Chem. Phys. 115, 3706 (2001) ], we analyze the HCN/CNH isomerizing molecule. We find that HCN/CNH has no monodromy and introduce the second global bending quantum number for this system at all energies where the potential is expected to work. We also show that LiNC/LiCN is a qualitatively different system with monodromy.
Evaluation of synthetic linear motor-molecule actuation energetics

PubMed Central

Brough, Branden; Northrop, Brian H.; Schmidt, Jacob J.; Tseng, Hsian-Rong; Houk, Kendall N.; Stoddart, J. Fraser; Ho, Chih-Ming

2006-01-01

By applying atomic force microscope (AFM)-based force spectroscopy together with computational modeling in the form of molecular force-field simulations, we have determined quantitatively the actuation energetics of a synthetic motor-molecule. This multidisciplinary approach was performed on specifically designed, bistable, redox-controllable [2]rotaxanes to probe the steric and electrostatic interactions that dictate their mechanical switching at the single-molecule level. The fusion of experimental force spectroscopy and theoretical computational modeling has revealed that the repulsive electrostatic interaction, which is responsible for the molecular actuation, is as high as 65 kcal·mol−1, a result that is supported by ab initio calculations. PMID:16735470
Multi-level study of C3H2: The first interstellar hydrocarbon ring

NASA Technical Reports Server (NTRS)

Madden, S. C.; Irvine, W. M.; Matthews, H. E.; Avery, L. W.

1986-01-01

Cyclic species in the interstellar medium have been searched for almost since the first detection of interstellar polyatomic molecules. Eleven different C3H2 rotational transitions were detected; 9 of which were studied in TMC-1, a nearby dark dust cloud, are shown. The 1 sub 10 yields 1 sub 01 and 2 sub 20 yields 2 sub 11 transitions were observed with the 43 m NRAO telescope, while the remaining transitions were detected with the 14 m antenna of the Five College Radio Observatory (FCRAO). The lines detected in TMC-1 have energies above the ground state ranging from 0.9 to 17.1 K and consist of both ortho and para species. Limited maps were made along the ridge for several of the transitions. The HC3N J = 2 yields 1 transition were mapped simultaneously with the C3H2 1 sub 10 yields 1 sub 01 line and therefore can compare the distribution of this ring with a carbon chain in TMC-1. C3H2 is distributed along a narrow ridge with a SE - NW extension which is slightly more extended than the HC2N J = 2 yields 1. Gaussian fits gives a FWHP extension of 8'5 for C3H2 while HC3N has a FWHP of 7'. The data show variations of the two velocity components along the ridge as a function of transition. Most of the transitions show a peak at the position of strongest HC3N emission while the 2 sub 21 yields 2 sub 10 transition shows a peak at the NH3 position.
Transport properties of partially ionized and unmagnetized plasmas.

PubMed

Magin, Thierry E; Degrez, Gérard

2004-10-01

This work is a comprehensive and theoretical study of transport phenomena in partially ionized and unmagnetized plasmas by means of kinetic theory. The pros and cons of different models encountered in the literature are presented. A dimensional analysis of the Boltzmann equation deals with the disparity of mass between electrons and heavy particles and yields the epochal relaxation concept. First, electrons and heavy particles exhibit distinct kinetic time scales and may have different translational temperatures. The hydrodynamic velocity is assumed to be identical for both types of species. Second, at the hydrodynamic time scale the energy exchanged between electrons and heavy particles tends to equalize both temperatures. Global and species macroscopic fluid conservation equations are given. New constrained integral equations are derived from a modified Chapman-Enskog perturbative method. Adequate bracket integrals are introduced to treat thermal nonequilibrium. A symmetric mathematical formalism is preferred for physical and numerical standpoints. A Laguerre-Sonine polynomial expansion allows for systems of transport to be derived. Momentum, mass, and energy fluxes are associated to shear viscosity, diffusion coefficients, thermal diffusion coefficients, and thermal conductivities. A Goldstein expansion of the perturbation function provides explicit expressions of the thermal diffusion ratios and measurable thermal conductivities. Thermal diffusion terms already found in the Russian literature ensure the exact mass conservation. A generalized Stefan-Maxwell equation is derived following the method of Kolesnikov and Tirskiy. The bracket integral reduction in terms of transport collision integrals is presented in Appendix for the thermal nonequilibrium case. A simple Eucken correction is proposed to deal with the internal degrees of freedom of atoms and polyatomic molecules, neglecting inelastic collisions. The authors believe that the final expressions are readily usable for practical applications in fluid dynamics.
Astrochemistry in TSR and CSR Ion Storage Rings

NASA Astrophysics Data System (ADS)

Novotny, Oldrich

2017-04-01

Dissociative recombination (DR) of molecular ions plays a key role in controlling the charge density and composition of the cold interstellar medium (ISM). Experimental data on DR are required in order to understand the chemical network in the ISM and related processes such as star formation from molecular clouds. Needed data include not only total reaction cross sections, but also the chemical composition and excitation states of the neutral products. Utilizing the TSR storage ring in Heidelberg, Germany, we have carried out DR measurements for astrophysically important molecular ions. We use a merged electron-ion beams technique combined with event-by-event fragment counting and fragment imaging. The count rate of detected neutral DR products yields the absolute DR rate coefficient. Imaging the distribution of fragment distances provides information on the kinetic energy released including the states of both the initial molecule and the final products. Additional kinetic energy sensitivity of the employed detector allows for identification of fragmentation channels by fragment-mass combination within each dissociation event. Such combined information is essential for studies on DR of polyatomic ions with multi-channel breakup. The recently commissioned Cryogenic Storage Ring (CSR) in Heidelberg, Germany, extends the experimental capabilities of TSR by operation at cryogenic temperatures down to 6 K. At these conditions residual gas densities down to 100 cm-3 can be reached resulting in beam storage times of several hours. Long storage in the cold environment allows the ions to relax down to their rotational ground state, thus mimicking well the conditions in the cold ISM. A variety of astrophysically relevant reactions will be investigated at these conditions, such as DR, electron impact excitation, ion-neutral collisions, etc. We report our TSR results on DR of HCl+ and D2Cl+. We also present first results from the CSR commissioning experiments.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Zeigler, N. R.; Zack, L. N.; Ziurys, L. M.

The J = 1 → 0 transition of HCO{sup +} at 89 GHz has been mapped across the Helix Nebula (NGC 7293) with 70'' spatial resolution (1.68 km s{sup –1} velocity resolution) using the Arizona Radio Observatory 12 m telescope. This work is the first large-scale mapping project of a dense gas tracer (n(H{sub 2}) ∼ 10{sup 5} cm{sup –3}) in old planetary nebulae. Observations of over 200 positions encompassing the classical optical image were conducted with a 3σ noise level of ∼20 mK. HCO{sup +} was detected at most positions, often exhibiting multiple velocity components indicative of complex kinematicmore » structures in dense gas. The HCO{sup +} spectra suggest that the Helix is composed of a bipolar, barrel-like structure with red- and blue-shifted halves, symmetric with respect to the central star and oriented ∼10° east from the line of sight. A second bipolar, higher velocity outflow exists as well, situated along the direction of the Helix 'plumes'. The column density of HCO{sup +} across the Helix is N {sub tot} ∼ 1.5 × 10{sup 10}-5.0 × 10{sup 11} cm{sup –2}, with an average value N {sub ave} ∼ 1 × 10{sup 11} cm{sup –2}, corresponding to an abundance, relative to H{sub 2}, of f ∼ 1.4 × 10{sup –8}. This value is similar to that observed in young PN, and contradicts chemical models, which predict that the abundance of HCO{sup +} decreases with nebular age. This study indicates that polyatomic molecules readily survive the ultraviolet field of the central white dwarf, and can be useful in tracing nebular morphology in the very late stages of stellar evolution.« less
A molecular theory of liquid interfaces.

PubMed

Kovalenko, Andriy; Hirata, Fumio

2005-04-21

We propose a site site generalization of the Lovett-Mow-Buff-Wertheim integro-differential equation for the one-particle density distributions to polyatomic fluids. The method provides microscopic description of liquid interfaces of molecular fluids and solutions. It uses the inhomogeneous site-site direct correlation function of molecular fluid consistently constructed by nonlinear interpolation between the homogeneous ones. The site site correlations of the coexisting bulk phases are obtained from the reference interaction site model (RISM) integral equation with our closure approximation. For illustration, we calculated the structure of the planar liquid-vapor as well as liquid-liquid interfaces of n-hexane and methanol at ambient conditions.
Watching cellular machinery in action, one molecule at a time.

PubMed

Monachino, Enrico; Spenkelink, Lisanne M; van Oijen, Antoine M

2017-01-02

Single-molecule manipulation and imaging techniques have become important elements of the biologist's toolkit to gain mechanistic insights into cellular processes. By removing ensemble averaging, single-molecule methods provide unique access to the dynamic behavior of biomolecules. Recently, the use of these approaches has expanded to the study of complex multiprotein systems and has enabled detailed characterization of the behavior of individual molecules inside living cells. In this review, we provide an overview of the various force- and fluorescence-based single-molecule methods with applications both in vitro and in vivo, highlighting these advances by describing their applications in studies on cytoskeletal motors and DNA replication. We also discuss how single-molecule approaches have increased our understanding of the dynamic behavior of complex multiprotein systems. These methods have shown that the behavior of multicomponent protein complexes is highly stochastic and less linear and deterministic than previously thought. Further development of single-molecule tools will help to elucidate the molecular dynamics of these complex systems both inside the cell and in solutions with purified components. © 2017 Monachino et al.
Visualization of DNA molecules in time during electrophoresis

NASA Technical Reports Server (NTRS)

Lubega, Seth

1991-01-01

For several years individual DNA molecules have been observed and photographed during agarose gel electrophoresis. The DNA molecule is clearly the largest molecule known. Nevertheless, the largest molecule is still too small to be seen using a microscope. A technique developed by Morikawa and Yanagida has made it possible to visualize individual DNA molecules. When these long molecules are labeled with appropriate fluorescence dyes and observed under a fluorescence microscope, although it is not possible to directly visualize the local ultrastructure of the molecules, yet because they are long light emitting chains, their microscopic dynamical behavior can be observed. This visualization works in the same principle that enables one to observe a star through a telescope because it emits light against a dark background. The dynamics of individual DNA molecules migrating through agarose matrix during electrophoresis have been described by Smith et al. (1989), Schwartz and Koval (1989), and Bustamante et al. (1990). DNA molecules during agarose gel electrophoresis advance lengthwise thorough the gel in an extended configuration. They display an extension-contraction motion and tend to bunch up in their leading ends as the 'heads' find new pores through the gel. From time to time they get hooked on obstacles in the gel to form U-shaped configurations before they resume their linear configuration.
Spin-orbit-coupled Bose-Einstein condensates of rotating polar molecules

NASA Astrophysics Data System (ADS)

Deng, Y.; You, L.; Yi, S.

2018-05-01

An experimental proposal for realizing spin-orbit (SO) coupling of pseudospin 1 in the ground manifold 1Σ (υ =0 ) of (bosonic) bialkali polar molecules is presented. The three spin components are composed of the ground rotational state and two substates from the first excited rotational level. Using hyperfine resolved Raman processes through two select excited states resonantly coupled by a microwave, an effective coupling between the spin tensor and linear momentum is realized. The properties of Bose-Einstein condensates for such SO-coupled molecules exhibiting dipolar interactions are further explored. In addition to the SO-coupling-induced stripe structures, the singly and doubly quantized vortex phases are found to appear, implicating exciting opportunities for exploring novel quantum physics using SO-coupled rotating polar molecules with dipolar interactions.
A linear biopolymer in the vicinity of the triple point. The homopolymer case.

PubMed

Frank-Kamenetskii, M D; Chogovadze, G I

1984-06-01

This is a theoretical study of a situation where each residue of a linear biopolymer may adopt one of three conformational states. Such a situation exists in the case of DNA, since it may be in helical A, B, . . ., Z forms as well as the melted state. In the vicinity of the triple point in the phrase diagram three states, e.g. the A form, the B form and the denatured state, co-exist within a given molecule. We present an exact analytical solution of the simplest homopolymer model. Theory predicts that the presence of two helical states in one molecule should affect the helix-coil transition in two ways. The melting temperature experiences an upward shift and the melting range width is increased, by a factor of square root of two as a maximum.
Design and Application of a High-Temperature Linear Ion Trap Reactor

NASA Astrophysics Data System (ADS)

Jiang, Li-Xue; Liu, Qing-Yu; Li, Xiao-Na; He, Sheng-Gui

2018-01-01

A high-temperature linear ion trap reactor with hexapole design was homemade to study ion-molecule reactions at variable temperatures. The highest temperature for the trapped ions is up to 773 K, which is much higher than those in available reports. The reaction between V2O6 - cluster anions and CO at different temperatures was investigated to evaluate the performance of this reactor. The apparent activation energy was determined to be 0.10 ± 0.02 eV, which is consistent with the barrier of 0.12 eV calculated by density functional theory. This indicates that the current experimental apparatus is prospective to study ion-molecule reactions at variable temperatures, and more kinetic details can be obtained to have a better understanding of chemical reactions that have overall barriers. [Figure not available: see fulltext.
Vanishing-Overhead Linear-Scaling Random Phase Approximation by Cholesky Decomposition and an Attenuated Coulomb-Metric.

PubMed

Luenser, Arne; Schurkus, Henry F; Ochsenfeld, Christian

2017-04-11

A reformulation of the random phase approximation within the resolution-of-the-identity (RI) scheme is presented, that is competitive to canonical molecular orbital RI-RPA already for small- to medium-sized molecules. For electronically sparse systems drastic speedups due to the reduced scaling behavior compared to the molecular orbital formulation are demonstrated. Our reformulation is based on two ideas, which are independently useful: First, a Cholesky decomposition of density matrices that reduces the scaling with basis set size for a fixed-size molecule by one order, leading to massive performance improvements. Second, replacement of the overlap RI metric used in the original AO-RPA by an attenuated Coulomb metric. Accuracy is significantly improved compared to the overlap metric, while locality and sparsity of the integrals are retained, as is the effective linear scaling behavior.
Crystal structure of zwitterionic bisimidazolium sulfonates

NASA Astrophysics Data System (ADS)

Kohmoto, Shigeo; Okuyama, Shinpei; Yokota, Nobuyuki; Takahashi, Masahiro; Kishikawa, Keiki; Masu, Hyuma; Azumaya, Isao

2012-05-01

Crystal structures of three zwitterionic bisimidazolium salts 1-3 in which imidazolium sulfonate moieties were connected with aromatic linkers, p-xylylene, 4,4'-dimethylenebiphenyl, and phenylene, respectively, were examined. The latter two were obtained as hydrates. An S-shaped molecular structure in which the sulfonate moiety was placed on the imidazolium ring was observed for 1. A helical array of hydrated water molecules was obtained for 2 while a linear array of hydrated water molecules was observed for 3.
Theoretical analysis of degradation mechanisms in the formation of morphogen gradients

NASA Astrophysics Data System (ADS)

Bozorgui, Behnaz; Teimouri, Hamid; Kolomeisky, Anatoly B.

2015-07-01

Fundamental biological processes of development of tissues and organs in multicellular organisms are governed by various signaling molecules, which are called morphogens. It is known that spatial and temporal variations in the concentration profiles of signaling molecules, which are frequently referred as morphogen gradients, lead to a cell differentiation via activating specific genes in a concentration-dependent manner. It is widely accepted that the establishment of the morphogen gradients involves multiple biochemical reactions and diffusion processes. One of the critical elements in the formation of morphogen gradients is a degradation of signaling molecules. We develop a new theoretical approach that provides a comprehensive description of the degradation mechanisms. It is based on the idea that the degradation works as an effective potential that drives the signaling molecules away from the source region. Utilizing the method of first-passage processes, the dynamics of the formation of morphogen gradients for various degradation mechanisms is explicitly evaluated. It is found that linear degradation processes lead to a dynamic behavior specified by times to form the morphogen gradients that depend linearly on the distance from the source. This is because the effective potential due to the degradation is quite strong. At the same time, nonlinear degradation mechanisms yield a quadratic scaling in the morphogen gradients formation times since the effective potentials are much weaker. Physical-chemical explanations of these phenomena are presented.
Tunable SERS signals of Rhodamine B molecules on Fe3O4@Au nanocomposite substrates controlled by magnetic field

NASA Astrophysics Data System (ADS)

Song, Hao; Fang, Rui Yang; Li, Ling

2018-02-01

In this work, we experimentally synthesized the Fe3O4@Au nanocomposites and used them as surface-enhanced Raman scattering (SERS) substrates. The Fe3O4@Au nanocomposites retained the metallic plasmon resonant effect and possessed the magnetic field controllable characteristics. The Raman spectra of Rhodamine B (RhB) probe molecules were studied under different external magnetic field. The magnitude of external magnetic field varied from 0 Gs to 700 Gs (1 Gs = 10-4 T) with intervals of 100 Gs. When the magnetic field magnitude increased, the Raman intensity of RhB probe molecules at 1356 cm-1 increased linearly. The slope of the linear fitting curves for the Raman intensity and area were 0.118/Gs and 3.700/Gs. The Raman enhancement could raise up to 7 times for RhB probe molecules when the magnetic field magnitude increased to 700 Gs. After removing the external magnetic field, the Raman peaks returned to its original intensity in several minutes. Under the external magnetic field, the Fe3O4@Au nanocomposites were concentrated, leading to the increase number of SERS "hot spots" and the surface Au density. The results show that the magnetic field controlled Fe3O4@Au nanocomposites can realize the enhanced and controllable SERS effect, which can be used in the reversible optical sensing and bio-medical applications.
Charge-transfer complexes of 2,3-dichloro-5,6-dicyano-1,4-benzoquinone with amino molecules in polar solvents

NASA Astrophysics Data System (ADS)

Berto, Silvia; Chiavazza, Enrico; Ribotta, Valentina; Daniele, Pier Giuseppe; Barolo, Claudia; Giacomino, Agnese; Vione, Davide; Malandrino, Mery

2015-10-01

The charge-transfer complexes have scientific relevance because this type of molecular interaction is at the basis of the activity of pharmacological compounds and because the absorption bands of the complexes can be used for the quantification of electron donor molecules. This work aims to assess the stability of the charge-transfer complexes between the electron acceptor 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) and two drugs, procaine and atenolol, in acetonitrile and ethanol. The stability of DDQ in solution and the time required to obtain the maximum complex formation were evaluated. The stoichiometry and the stability of the complexes were determined, respectively, by Job's plot method and by the elaboration of UV-vis titrations data. The latter task was carried out by using the non-linear global analysis approach to determine the equilibrium constants. This approach to data elaboration allowed us to overcome the disadvantages of the classical linear-regression method, to obtain reliable values of the association constants and to calculate the entire spectra of the complexes. NMR spectra were recorded to identify the portion of the donor molecule that was involved in the interaction. The data support the participation of the aliphatic amino groups in complex formation and exclude the involvement of the aromatic amine present in the procaine molecule.
The mitochondrial genome of the pathogenic yeast Candida subhashii: GC-rich linear DNA with a protein covalently attached to the 5′ termini

PubMed Central

Fricova, Dominika; Valach, Matus; Farkas, Zoltan; Pfeiffer, Ilona; Kucsera, Judit; Tomaska, Lubomir; Nosek, Jozef

2010-01-01

As a part of our initiative aimed at a large-scale comparative analysis of fungal mitochondrial genomes, we determined the complete DNA sequence of the mitochondrial genome of the yeast Candida subhashii and found that it exhibits a number of peculiar features. First, the mitochondrial genome is represented by linear dsDNA molecules of uniform length (29 795 bp), with an unusually high content of guanine and cytosine residues (52.7 %). Second, the coding sequences lack introns; thus, the genome has a relatively compact organization. Third, the termini of the linear molecules consist of long inverted repeats and seem to contain a protein covalently bound to terminal nucleotides at the 5′ ends. This architecture resembles the telomeres in a number of linear viral and plasmid DNA genomes classified as invertrons, in which the terminal proteins serve as specific primers for the initiation of DNA synthesis. Finally, although the mitochondrial genome of C. subhashii contains essentially the same set of genes as other closely related pathogenic Candida species, we identified additional ORFs encoding two homologues of the family B protein-priming DNA polymerases and an unknown protein. The terminal structures and the genes for DNA polymerases are reminiscent of linear mitochondrial plasmids, indicating that this genome architecture might have emerged from fortuitous recombination between an ancestral, presumably circular, mitochondrial genome and an invertron-like element. PMID:20395267
Determination and importance of temperature dependence of retention coefficient (RPHPLC) in QSAR model of nitrazepams' partition coefficient in bile acid micelles.

PubMed

Posa, Mihalj; Pilipović, Ana; Lalić, Mladena; Popović, Jovan

2011-02-15

Linear dependence between temperature (t) and retention coefficient (k, reversed phase HPLC) of bile acids is obtained. Parameters (a, intercept and b, slope) of the linear function k=f(t) highly correlate with bile acids' structures. Investigated bile acids form linear congeneric groups on a principal component (calculated from k=f(t)) score plot that are in accordance with conformations of the hydroxyl and oxo groups in a bile acid steroid skeleton. Partition coefficient (K(p)) of nitrazepam in bile acids' micelles is investigated. Nitrazepam molecules incorporated in micelles show modified bioavailability (depo effect, higher permeability, etc.). Using multiple linear regression method QSAR models of nitrazepams' partition coefficient, K(p) are derived on the temperatures of 25°C and 37°C. For deriving linear regression models on both temperatures experimentally obtained lipophilicity parameters are included (PC1 from data k=f(t)) and in silico descriptors of the shape of a molecule while on the higher temperature molecular polarisation is introduced. This indicates the fact that the incorporation mechanism of nitrazepam in BA micelles changes on the higher temperatures. QSAR models are derived using partial least squares method as well. Experimental parameters k=f(t) are shown to be significant predictive variables. Both QSAR models are validated using cross validation and internal validation method. PLS models have slightly higher predictive capability than MLR models. Copyright © 2010 Elsevier B.V. All rights reserved.

Chemical structure-nonlinear optical property relationships for a series of two-photon absorbing fluorene molecules

NASA Astrophysics Data System (ADS)

Hales, Joel Mccajah

This dissertation reports on the investigation of two-photon absorption (2PA) in a series of fluorenyl molecules. Several current and emerging technologies exploit this optical nonlinearity including two-photon fluorescence imaging, three-dimensional microfabrication, site-specific photodynamic cancer therapy and biological caging studies. The two key features of this nonlinearity which make it an ideal candidate for the above applications are its quadratic dependence on the incident irradiance and the improved penetration into absorbing media that it affords. As a consequence of the burgeoning field which exploits 2PA, it is a goal to find materials that exhibit strong two-photon absorbing capabilities. Organic materials are promising candidates for 2PA applications because their material properties can be tailored through molecular engineering thereby facilitating optimization of their nonlinear optical properties. Fluorene derivatives are particularly interesting since they possess high photochemical stability for organic molecules and are generally strongly fluorescent. By systematically altering the structural properties in a series of fluorenyl molecules, we have determined how these changes affect their two-photon absorbing capabilities. This was accomplished through characterization of both the strength and location of their 2PA spectra. In order to ensure the validity of these results, three separate nonlinear characterization techniques were employed: two-photon fluorescence spectroscopy, white-light continuum pump-probe spectroscopy, and the Z-scan technique. In addition, full linear spectroscopic characterization was performed on these molecules along with supplementary quantum chemical calculations to obtain certain molecular properties that might impact the nonlinearity. Different designs in chemical architecture allowed investigation of the effects of symmetry, solvism, donor-acceptor strengths, conjugation length, and multi-branched geometries on the two-photon absorbing properties of these molecules. In addition, the means to enhance 2PA via intermediate state resonances was investigated. To provide plausible explanations for the experimentally observed trends, a conceptually simple three level model was employed. The subsequent correlations found between chemical structure and the linear and nonlinear optical properties of these molecules provided definitive conclusions on how to properly optimize their two-photon absorbing capabilities. The resulting large nonlinearities found in these molecules have already shown promise in a variety of the aforementioned applications.
Development of a reference material of a single DNA molecule for the quality control of PCR testing.

PubMed

Mano, Junichi; Hatano, Shuko; Futo, Satoshi; Yoshii, Junji; Nakae, Hiroki; Naito, Shigehiro; Takabatake, Reona; Kitta, Kazumi

2014-09-02

We developed a reference material of a single DNA molecule with a specific nucleotide sequence. The double-strand linear DNA which has PCR target sequences at the both ends was prepared as a reference DNA molecule, and we named the PCR targets on each side as confirmation sequence and standard sequence. The highly diluted solution of the reference molecule was dispensed into 96 wells of a plastic PCR plate to make the average number of molecules in a well below one. Subsequently, the presence or absence of the reference molecule in each well was checked by real-time PCR targeting for the confirmation sequence. After an enzymatic treatment of the reaction mixture in the positive wells for the digestion of PCR products, the resultant solution was used as the reference material of a single DNA molecule with the standard sequence. PCR analyses revealed that the prepared samples included only one reference molecule with high probability. The single-molecule reference material developed in this study will be useful for the absolute evaluation of a detection limit of PCR-based testing methods, the quality control of PCR analyses, performance evaluations of PCR reagents and instruments, and the preparation of an accurate calibration curve for real-time PCR quantitation.
Singlet fission in linear chains of molecules

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

Ambrosio, Francesco, E-mail: F.Ambrosio@warwick.ac.uk, E-mail: A.Troisi@warwick.ac.uk; Troisi, Alessandro, E-mail: F.Ambrosio@warwick.ac.uk, E-mail: A.Troisi@warwick.ac.uk

2014-11-28

We develop a model configuration interaction Hamiltonian to study the electronic structure of a chain of molecules undergoing singlet fission. We first consider models for dimer and trimer and then we use a matrix partitioning technique to build models of arbitrary size able to describe the relevant electronic structure for singlet fission in linear aggregates. We find that the multi-excitonic state (ME) is stabilized at short inter-monomer distance and the extent of this stabilization depends upon the size of orbital coupling between neighboring monomers. We also find that the coupling between ME states located on different molecules is extremely smallmore » leading to bandwidths in the order of ∼10 meV. This observation suggests that multi-exciton states are extremely localized by electron-phonon coupling and that singlet fission involves the transition between a relatively delocalized Frenkel exciton and a strongly localized multi-exciton state. We adopt the methodology commonly used to study non-radiative transitions to describe the singlet fission dynamics in these aggregates and we discuss the limit of validity of the approach. The results indicate that the phenomenology of singlet fission in molecular crystals is different in many important ways from what is observed in isolated dimers.« less
Quantitative nanoimmunosensor based on dark-field illumination with enhanced sensitivity and on-off switching using scattering signals.

PubMed

Lee, Seungah; Nan, He; Yu, Hyunung; Kang, Seong Ho

2016-05-15

A nanoimmunosensor based on wavelength-dependent dark-field illumination with enhanced sensitivity was used to detect a disease-related protein molecule at zeptomolar (zM) concentrations. The assay platform of 100-nm gold nanospots could be selectively acquired using the wavelength-dependence of enhanced scattering signals from antibody-conjugated plasmonic silver nanoparticles (NPs) with on-off switching using optical filters. Detection of human thyroid-stimulating hormone (hTSH) at a sensitivity of 100 zM, which corresponds to 1-2 molecules per gold spot, was possible within a linear range of 100 zM-100 fM (R=0.9968). A significantly enhanced sensitivity (~4-fold) was achieved with enhanced dark-field illumination compared to using a total internal reflection fluorescence immunosensor. Immunoreactions were confirmed via optical axial-slicing based on the spectral characteristics of two plasmonic NPs. This method of using wavelength-dependent dark-field illumination had an enhanced sensitivity and a wide, linear dynamic range of 100 zM-100 fM, and was an effective tool for quantitatively detecting a single molecule on a nanobiochip for molecular diagnostics. Copyright © 2016 Elsevier B.V. All rights reserved.
A theoretical perspective of the nature of hydrogen-bond types - the atoms in molecules approach

NASA Astrophysics Data System (ADS)

Vijaya Pandiyan, B.; Kolandaivel, P.; Deepa, P.

2014-06-01

Hydrogen bonds and their strength were analysed based on their X-H proton-donor bond properties and the parameters of the H-Y distance (Y proton acceptor). Strong, moderate and weak interactions in hydrogen-bond types were verified through the proton affinities of bases (PA), deprotanation enthalpies of acids (DPE) and the chemical shift (σ). The aromaticity and anti-aromaticity were analysed by means of the NICS (0) (nucleus-independent chemical shift), NICS (1) and ΔNICS (0), ΔNICS (1) of hydrogen-bonded molecules. The strength of a hydrogen bond depends on the capacity of hydrogen atom engrossing into the electronegative acceptor atom. The correlation between the above parameters and their relations were discussed through curve fitting. Bader's theory of atoms in molecules has been applied to estimate the occurrence of hydrogen bonds through eight criteria reported by Popelier et al. The lengths and potential energy shifts have been found to have a strong negative linear correlation, whereas the lengths and Laplacian shifts have a strong positive linear correlation. This study illustrates the common factors responsible for strong, moderate and weak interactions in hydrogen-bond types.
Optical detection of glucose and glycated hemoglobin using etched fiber Bragg gratings coated with functionalized reduced graphene oxide.

PubMed

Sridevi, S; Vasu, K S; Sampath, S; Asokan, S; Sood, A K

2016-07-01

An enhanced optical detection of D-glucose and glycated hemoglobin (HbA1c ) has been established in this study using etched fiber Bragg gratings (eFBG) coated with aminophenylboronic acid (APBA)-functionalized reduced graphene oxide (RGO). The read out, namely the shift in Bragg wavelength (ΔλB ) is highly sensitive to changes that occur due to the adsorption of glucose (or HbA1c ) molecules on the eFBG sensor coated with APBA-RGO complex through a five-membered cyclic ester bond formation between glucose and APBA molecules. A limit of detection of 1 nM is achieved with a linear range of detection from 1 nM to 10 mM in the case of D-glucose detection experiments. For HbA1c , a linear range of detection varying from 86 nM to 0.23 mM is achieved. The observation of only 4 pm (picometer) change in ΔλB even for the 10 mM lactose solution confirms the specificity of the APBA-RGO complex coated eFBG sensors to glucose molecules. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Efficient parallel linear scaling construction of the density matrix for Born-Oppenheimer molecular dynamics.

PubMed

Mniszewski, S M; Cawkwell, M J; Wall, M E; Mohd-Yusof, J; Bock, N; Germann, T C; Niklasson, A M N

2015-10-13

We present an algorithm for the calculation of the density matrix that for insulators scales linearly with system size and parallelizes efficiently on multicore, shared memory platforms with small and controllable numerical errors. The algorithm is based on an implementation of the second-order spectral projection (SP2) algorithm [ Niklasson, A. M. N. Phys. Rev. B 2002 , 66 , 155115 ] in sparse matrix algebra with the ELLPACK-R data format. We illustrate the performance of the algorithm within self-consistent tight binding theory by total energy calculations of gas phase poly(ethylene) molecules and periodic liquid water systems containing up to 15,000 atoms on up to 16 CPU cores. We consider algorithm-specific performance aspects, such as local vs nonlocal memory access and the degree of matrix sparsity. Comparisons to sparse matrix algebra implementations using off-the-shelf libraries on multicore CPUs, graphics processing units (GPUs), and the Intel many integrated core (MIC) architecture are also presented. The accuracy and stability of the algorithm are illustrated with long duration Born-Oppenheimer molecular dynamics simulations of 1000 water molecules and a 303 atom Trp cage protein solvated by 2682 water molecules.
Identifying the Molecular Origin of Global Warming

NASA Technical Reports Server (NTRS)

Bera, Partha P.; Francisco, Joseph S.; Lee, Timothy J.

2009-01-01

We have investigated the physical characteristics of greenhouse gases (GHGs) to assess which properties are most important in determining the efficiency of a GHG. Chlorofluorcarbons (CFCs), hydrofluorocarbons (HFCs), perfluorocarbons (PFCs), nitrogen fluorides, and various other known atmospheric trace molecules have been included in this study. Compounds containing the halogens F or Cl have in common very polar X-F or X-Cl bonds, particularly the X-F bonds. It is shown that as more F atoms bond to the same central atom, the bond dipoles become larger as a result of the central atom becoming more positive. This leads to a linear increase in the total or integrated XF bond dipole derivatives for the molecule, which leads to a non-linear (quadratic) increase in infrared (IR) intensity. Moreover, virtually all of the X-F bond stretches occur in the atmospheric IR window as opposed to X-H stretches, which do not occur in the atmospheric window. It is concluded that molecules possessing several F atoms will always have a large radiative forcing parameter in the calculation of their global warming potential. Some of the implications for global warming and climate change are discussed.
Dispersion interactions with linear scaling DFT: a study of planar molecules on charged polar surfaces

NASA Astrophysics Data System (ADS)

Andrinopoulos, Lampros; Hine, Nicholas; Haynes, Peter; Mostofi, Arash

2010-03-01

The placement of organic molecules such as CuPc (copper phthalocyanine) on wurtzite ZnO (zinc oxide) charged surfaces has been proposed as a way of creating photovoltaic solar cellsfootnotetextG.D. Sharma et al., Solar Energy Materials & Solar Cells 90, 933 (2006) ; optimising their performance may be aided by computational simulation. Electronic structure calculations provide high accuracy at modest computational cost but two challenges are encountered for such layered systems. First, the system size is at or beyond the limit of traditional cubic-scaling Density Functional Theory (DFT). Second, traditional exchange-correlation functionals do not account for van der Waals (vdW) interactions, crucial for determining the structure of weakly bonded systems. We present an implementation of recently developed approachesfootnotetextP.L. Silvestrelli, P.R.L. 100, 102 (2008) to include vdW in DFT within ONETEPfootnotetextC.-K. Skylaris, P.D. Haynes, A.A. Mostofi and M.C. Payne, J.C.P. 122, 084119 (2005) , a linear-scaling package for performing DFT calculations using a basis of localised functions. We have applied this methodology to simple planar organic molecules, such as benzene and pentacene, on ZnO surfaces.
Room temperature structures and odd even behaviour of a homologous series of anhydrous lithium n-alkanoates

NASA Astrophysics Data System (ADS)

White, Nicole A. S.; Ellis, Henry A.

2008-10-01

The molecular structures of a homologous series of lithium n-alkanoates have been determined at room temperature using infrared spectroscopy, polarizing light microscopy and X-ray powder diffraction in conjunction with density and melting point measurements. For all the compounds investigated, asymmetric ionic metal-carboxylate coordination is proposed, with the molecules located within a triclinic crystal system with P1¯ space group. The molecules are nearly all of similar structure and are arranged within lamellar layers with four molecules per unit cell. The hydrocarbon chains, in nearly all trans conformation, are arranged tail-to-tail and tilted at an average angle of 55 ο to the planes containing lithium ions. The unit cell parameters such as sides: b and c increase linearly with increasing chain length whilst side a shows a linear decrease. Furthermore, the measured densities and melting points show odd-even behaviour, suggesting differences in molecular packing between odd and even chain length homologues. Geometric models are proposed to explain molecular orientation within a lamella and odd-even behaviour, involving the influence of terminal groups on the packing geometry of hydrocarbon chains within the lattice.
Experimental observation and determination of the laser-induced frequency shift of hyperfine levels of ultracold polar molecules

NASA Astrophysics Data System (ADS)

Liu, Wenliang; Wang, Xiaofeng; Wu, Jizhou; Su, Xingliang; Wang, Shen; Sovkov, Vladimir B.; Ma, Jie; Xiao, Liantuan; Jia, Suotang

2017-08-01

We report on the experimental observation and quantitative determination of the laser-induced frequency shift (LIFS) of the ultracold polar molecules formed by photoassociation (PA). The experiments are performed by detecting a series of double PA spectra with a molecular hyperfine structure, which are induced by two PA lasers with a precise and adjustable frequency reference. We find that the LIFS of the molecular hyperfine levels shows a linear dependence on PA laser intensity.
Electrically controllable photonic molecule laser.

PubMed

Fasching, G; Deutsch, Ch; Benz, A; Andrews, A M; Klang, P; Zobl, R; Schrenk, W; Strasser, G; Ragulis, P; Tamosiūnas, V; Unterrainer, K

2009-10-26

We have studied the coherent intercavity coupling of the evanescent fields of two microdisk terahertz quantum-cascade lasers. The electrically controllable optical coupling of the single-mode operating lasers has been observed for cavity spacings up to 30 mum. The strongest coupled photonic molecule with 2 mum intercavity spacing allows to conditionally switch the optical emission by the electrical modulation of only one microdisk. The lasing threshold characteristics demonstrate the linear dependence of the gain of a quantum-cascade laser on the applied electric field.
Self-assembly of heterogeneous supramolecular structures with uniaxial anisotropy.

PubMed

Ruiz-Osés, M; Gonzalez-Lakunza, N; Silanes, I; Gourdon, A; Arnau, A; Ortega, J E

2006-12-28

Uniaxial anisotropy in two-dimensional self-assembled supramolecular structures is achieved by the coadsorption of two different linear molecules with complementary amine and imide functionalization. The two-dimensional monolayer is defined by a one-dimensional stack of binary chains, which can be forced to line up along steps in vicinal surfaces. The competing driving forces in the self-organization process are discussed in light of the structures observed during single molecule adsorption and coadsorption on flat and vicinal surfaces and the corresponding theoretical calculations.
Communication: Finding destructive interference features in molecular transport junctions.

PubMed

Reuter, Matthew G; Hansen, Thorsten

2014-11-14

Associating molecular structure with quantum interference features in electrode-molecule-electrode transport junctions has been difficult because existing guidelines for understanding interferences only apply to conjugated hydrocarbons. Herein we use linear algebra and the Landauer-Büttiker theory for electron transport to derive a general rule for predicting the existence and locations of interference features. Our analysis illustrates that interferences can be directly determined from the molecular Hamiltonian and the molecule-electrode couplings, and we demonstrate its utility with several examples.
Nonlinear vs. linear biasing in Trp-cage folding simulations

NASA Astrophysics Data System (ADS)

Spiwok, Vojtěch; Oborský, Pavel; Pazúriková, Jana; Křenek, Aleš; Králová, Blanka

2015-03-01

Biased simulations have great potential for the study of slow processes, including protein folding. Atomic motions in molecules are nonlinear, which suggests that simulations with enhanced sampling of collective motions traced by nonlinear dimensionality reduction methods may perform better than linear ones. In this study, we compare an unbiased folding simulation of the Trp-cage miniprotein with metadynamics simulations using both linear (principle component analysis) and nonlinear (Isomap) low dimensional embeddings as collective variables. Folding of the mini-protein was successfully simulated in 200 ns simulation with linear biasing and non-linear motion biasing. The folded state was correctly predicted as the free energy minimum in both simulations. We found that the advantage of linear motion biasing is that it can sample a larger conformational space, whereas the advantage of nonlinear motion biasing lies in slightly better resolution of the resulting free energy surface. In terms of sampling efficiency, both methods are comparable.
Nonlinear vs. linear biasing in Trp-cage folding simulations.

PubMed

Spiwok, Vojtěch; Oborský, Pavel; Pazúriková, Jana; Křenek, Aleš; Králová, Blanka

2015-03-21

Biased simulations have great potential for the study of slow processes, including protein folding. Atomic motions in molecules are nonlinear, which suggests that simulations with enhanced sampling of collective motions traced by nonlinear dimensionality reduction methods may perform better than linear ones. In this study, we compare an unbiased folding simulation of the Trp-cage miniprotein with metadynamics simulations using both linear (principle component analysis) and nonlinear (Isomap) low dimensional embeddings as collective variables. Folding of the mini-protein was successfully simulated in 200 ns simulation with linear biasing and non-linear motion biasing. The folded state was correctly predicted as the free energy minimum in both simulations. We found that the advantage of linear motion biasing is that it can sample a larger conformational space, whereas the advantage of nonlinear motion biasing lies in slightly better resolution of the resulting free energy surface. In terms of sampling efficiency, both methods are comparable.
Dynamics of osmosis in a porous medium.

PubMed

Cardoso, Silvana S S; Cartwright, Julyan H E

2014-11-01

We derive from kinetic theory, fluid mechanics and thermodynamics the minimal continuum-level equations governing the flow of a binary, non-electrolytic mixture in an isotropic porous medium with osmotic effects. For dilute mixtures, these equations are linear and in this limit provide a theoretical basis for the widely used semi-empirical relations of Kedem & Katchalsky (Kedem & Katchalsky 1958 Biochim. Biophys. Acta 27, 229-246 (doi:10.1016/0006-3002(58)90330-5), which have hitherto been validated experimentally but not theoretically. The above linearity between the fluxes and the driving forces breaks down for concentrated or non-ideal mixtures, for which our equations go beyond the Kedem-Katchalsky formulation. We show that the heretofore empirical solute permeability coefficient reflects the momentum transfer between the solute molecules that are rejected at a pore entrance and the solvent molecules entering the pore space; it can be related to the inefficiency of a Maxwellian demi-demon.
Tailoring magnetic nanoparticle for transformers application.

PubMed

Morais, P C; Silva, A S; Leite, E S; Garg, V K; Oliveira, A C; Viali, W R; Sartoratto, P P C

2010-02-01

In this study photoacoustic spectroscopy was used to investigate the effect of dilution of an oil-based magnetic fluid sample on the magnetic nanoparticle surface-coating. Changes of the photoacoustic signal intensity on the band-L region (640 to 830 nm) upon dilution of the stock magnetic fluid sample were discussed in terms of molecular surface desorption. The model proposed here assumes that the driving force taking the molecules out from the nanoparticle surface into the bulk solvent is the gradient of osmotic pressure. This gradient of osmotic pressure is established between the nanoparticle surface and the bulk suspension. It is further assumed that the photoacoustic signal intensity (area under the photoacoustic spectra) scales linearly with the number of coating molecules (surface grafting) at the nanoparticle surface. This model picture provides a non-linear analytical description for the reduction of the surface grafting coefficient upon dilution, which was successfully-used to curve-fit the photoacoustic experimental data.
Life Before RNA

NASA Astrophysics Data System (ADS)

Sowerby, Stephen J.; Petersen, George B.

2002-08-01

The hypothesis that life originated and evolved from linear informational molecules capable of facilitating their own catalytic replication is deeply entrenched. However, widespread acceptance of this paradigm seems oblivious to a lack of direct experimental support. Here, we outline the fundamental objections to the de novo appearance of linear, self-replicating polymers and examine an alternative hypothesis of template-directed coding of peptide catalysts by adsorbed purine bases. The bases (which encode biological information in modern nucleic acids) spontaneously self-organize into two-dimensional molecular solids adsorbed to the uncharged surfaces of crystalline minerals; their molecular arrangement is specified by hydrogen bonding rules between adjacent molecules and can possess the aperiodic complexity to encode putative protobiological information. The persistence of such information through self-reproduction, together with the capacity of adsorbed bases to exhibit enantiomorphism and effect amino acid discrimination, would seem to provide the necessary machinery for a primitive genetic coding mechanism.
The hydrodeoxygenation of bioderived furans into alkanes.

PubMed

Sutton, Andrew D; Waldie, Fraser D; Wu, Ruilian; Schlaf, Marcel; Silks, Louis A Pete; Gordon, John C

2013-05-01

The conversion of biomass into fuels and chemical feedstocks is one part of a drive to reduce the world's dependence on crude oil. For transportation fuels in particular, wholesale replacement of a fuel is logistically problematic, not least because of the infrastructure that is already in place. Here, we describe the catalytic defunctionalization of a series of biomass-derived molecules to provide linear alkanes suitable for use as transportation fuels. These biomass-derived molecules contain a variety of functional groups, including olefins, furan rings and carbonyl groups. We describe the removal of these in either a stepwise process or a one-pot process using common reagents and catalysts under mild reaction conditions to provide n-alkanes in good yields and with high selectivities. Our general synthetic approach is applicable to a range of precursors with different carbon content (chain length). This allows the selective generation of linear alkanes with carbon chain lengths between eight and sixteen carbons.

Some links on this page may take you to non-federal websites. Their policies may differ from this site.