scholarly journals Theoretical Characterization of Transition State Dynamical Resonances in Heavy–Light–Heavy Reactions

1991 ◽  
Vol 11 (3-4) ◽  
pp. 291-302
Author(s):  
A. Aguilar ◽  
M. Albertí ◽  
R. Blasco ◽  
M. Gilibert ◽  
X. Giménez ◽  
...  
Keyword(s):  
Transition State ◽  
Cross Sections ◽  
Energy Surface ◽  
Three Dimensional ◽  
Direct Consequence ◽  
Resonant Peak ◽  
S Matrix ◽  
Energy Dependent ◽  
Argand Plot

The resonant reactivity of three elementary Heavy–Light–Heavy reactions is presented and discussed. Collinear reactivity, in which a vibrational adiabatic model is constructed, is used for a detailed analysis of resonance phenomena, which appear as a direct consequence of transition state metastable states in the strong interaction region of the potential energy surface. Their influence on the detailed mechanism of the elementary process is also discussed. The shape of the resonant peak, and the phase and the Argand plot of the S-matrix are used for a further characterization.Three-dimensional approximate calculations are used to test the evolution of the energy dependent structure present in detailed quantities when sums and integrations over all partial waves contributing to reaction are taken into account to obtain the usual averaged global quantities such as integral state-to-state cross sections.

Collision excitation of sodium cyanide molecule by helium at low temperature

2019 ◽  
Vol 489 (3) ◽  
pp. 4322-4328
Author(s):  
C Gharbi ◽  
Y Ajili ◽  
D Ben Abdallah ◽  
M Mogren Al Mogren ◽  
M Hochlaf
Keyword(s):  
Electronic Structure ◽  
Cross Sections ◽  
Energy Surface ◽  
Three Dimensional ◽  
Sodium Cyanide ◽  
Rate Coefficients ◽  
Quantum Scattering ◽  
Stable Form ◽  
Excitation Cross Sections ◽  
Order Of Magnitude

ABSTRACT Cyanides/isocyanides are the most common metal-containing molecules in interstellar medium. In this work, quantum scattering calculations were carried out to determine the rotational (de-)excitation cross-sections of the most stable form of the sodium cyanide molecule, t-NaCN, in collision with the helium atom. Rate coefficients for the first 43 rotational levels (up to ${j_{{K_a}{K_c}}}$ = 63,3) of NaCN were determined for kinetic temperatures ranging from 1 to 30 K. Prior to that, we constructed a new three-dimensional potential energy surface (3D-PES) for the t-NaCN–He interacting system. These electronic structure computations are done at the CCSD(T)-F12/aug-cc-pVTZ level of theory. Computations show the dominance of Δj = ΔKc = −1 transitions, which is related to the dissymmetric shape of the t-NaCN–He 3D-PES. The NaCN–He rate coefficients are of the same order of magnitude (∼10−11 cm3.s−1) as those of other metal CN-containing molecules such as MgCN and AlCN in collision with He. This work is a contribution for understanding and modelling the abundances and chemistry of nitriles in astrophysical media.

QUANTUM DYNAMICS OF THE He + Li2 INELASTIC SCATTERING

2011 ◽  
Vol 10 (03) ◽  
pp. 297-307
Author(s):  
SINAN AKPINAR ◽  
TUNAY TURMUS ◽  
SEDA SURUCU
Keyword(s):  
Wave Packet ◽  
Cross Sections ◽  
Quantum Dynamics ◽  
Total Angular Momentum ◽  
Collision Energy ◽  
Energy Surface ◽  
Transition Probabilities ◽  
Three Dimensional ◽  
Quantum Wave ◽  
Inelastic Reaction

In this paper, we report the results of three dimensional time dependent quantum wave packet calculations carried out for He+Li2 inelastic reaction in the collision energy range 0.43–1.18 eV. A three dimensional potential energy surface (PES) computed by Varandas was used for the dynamical calculations.1 The state to state and state to all transition probabilities for total angular momentum J = 0 have been calculated in a broad range of collision energies. Integral cross-sections and rate constants have been calculated from the wave packet transition probabilities by means of J-shifting approximation based on a capture model and a uniform J-shifting method for J > 0.

SIGMAL: A Program for Calculating L-Shell lonization Cross-Sections

1981 ◽  
Vol 39 ◽  
pp. 198-199 ◽  
Author(s):  
R.F. Egerton
Keyword(s):  
Cross Sections ◽  
Fortran Program ◽  
Absorption Data ◽  
X Ray ◽  
Atomic Electrons ◽  
Energy Dependent ◽  
Hydrogenic Model ◽  
Electron Energy Loss ◽  
X Ray Absorption ◽  
Shell Ionization

SIGMAL is a short (∼ 100-line) Fortran program designed to rapidly compute cross-sections for L-shell ionization, particularly the partial crosssections required in quantitative electron energy-loss microanalysis. The program is based on a hydrogenic model, the L1 and L23 subshells being represented by scaled Coulombic wave functions, which allows the generalized oscillator strength (GOS) to be expressed analytically. In this basic form, the model predicts too large a cross-section at energies near to the ionization edge (see Fig. 1), due mainly to the fact that the screening effect of the atomic electrons is assumed constant over the L-shell region. This can be remedied by applying an energy-dependent correction to the GOS or to the effective nuclear charge, resulting in much closer agreement with experimental X-ray absorption data and with more sophisticated calculations (see Fig. 1 ).

Characterization of photosystem II with the atomic-force microscope

1992 ◽  
Vol 50 (2) ◽  
pp. 1146-1147
Author(s):  
Kathleen M. Marr ◽  
Mary K. Lyon
Keyword(s):  
Photosystem Ii ◽  
Atomic Force Microscope ◽  
Three Dimensional ◽  
Biologically Active ◽  
Atomic Force ◽  
Freeze Etching ◽  
Image Averaging ◽  
Oxygen Evolving ◽  
Averaging Techniques

Photosystem II (PSII) is different from all other reaction centers in that it splits water to evolve oxygen and hydrogen ions. This unique ability to evolve oxygen is partly due to three oxygen evolving polypeptides (OEPs) associated with the PSII complex. Freeze etching on grana derived insideout membranes revealed that the OEPs contribute to the observed tetrameric nature of the PSIl particle; when the OEPs are removed, a distinct dimer emerges. Thus, the surface of the PSII complex changes dramatically upon removal of these polypeptides. The atomic force microscope (AFM) is ideal for examining surface topography. The instrument provides a topographical view of individual PSII complexes, giving relatively high resolution three-dimensional information without image averaging techniques. In addition, the use of a fluid cell allows a biologically active sample to be maintained under fully hydrated and physiologically buffered conditions. The OEPs associated with PSII may be sequentially removed, thereby changing the surface of the complex by one polypeptide at a time.

convergent-beam diffraction from surfaces

1987 ◽  
Vol 45 ◽  
pp. 30-33
Author(s):  
J. A. Eades ◽  
A. E. Smith ◽  
D. F. Lynch
Keyword(s):  
Reciprocal Lattice ◽  
Three Dimensional ◽  
Grazing Incidence ◽  
Three Dimensions ◽  
Plane Figure ◽  
Transmission Electron ◽  
Convergent Beam ◽  
Beam Patterns ◽  
Beam Diffraction

It is quite simple (in the transmission electron microscope) to obtain convergent-beam patterns from the surface of a bulk crystal. The beam is focussed onto the surface at near grazing incidence (figure 1) and if the surface is flat the appropriate pattern is obtained in the diffraction plane (figure 2). Such patterns are potentially valuable for the characterization of surfaces just as normal convergent-beam patterns are valuable for the characterization of crystals.There are, however, several important ways in which reflection diffraction from surfaces differs from the more familiar electron diffraction in transmission.GeometryIn reflection diffraction, because of the surface, it is not possible to describe the specimen as periodic in three dimensions, nor is it possible to associate diffraction with a conventional three-dimensional reciprocal lattice.

Construction of plastic contact deformation maps on ceramics: a case study on aluminum nitride

1996 ◽  
Vol 54 ◽  
pp. 636-637
Author(s):  
D. L. Callahan
Keyword(s):  
Plastic Deformation ◽  
Aluminum Nitride ◽  
Mechanical Response ◽  
Three Dimensional ◽  
Bright Field Image ◽  
Perfectly Plastic ◽  
Contrast Analysis ◽  
Deformation Patterns

Modern polishing, precision machining and microindentation techniques allow the processing and mechanical characterization of ceramics at nanometric scales and within entirely plastic deformation regimes. The mechanical response of most ceramics to such highly constrained contact is not predictable from macroscopic properties and the microstructural deformation patterns have proven difficult to characterize by the application of any individual technique. In this study, TEM techniques of contrast analysis and CBED are combined with stereographic analysis to construct a three-dimensional microstructure deformation map of the surface of a perfectly plastic microindentation on macroscopically brittle aluminum nitride.The bright field image in Figure 1 shows a lg Vickers microindentation contained within a single AlN grain far from any boundaries. High densities of dislocations are evident, particularly near facet edges but are not individually resolvable. The prominent bend contours also indicate the severity of plastic deformation. Figure 2 is a selected area diffraction pattern covering the entire indentation area.

Characterization of a monolayer graphitic structure

1994 ◽  
Vol 52 ◽  
pp. 760-761
Author(s):  
X. Lin ◽  
X. K. Wang ◽  
V. P. Dravid ◽  
J. B. Ketterson ◽  
R. P. H. Chang
Keyword(s):  
Three Dimensional ◽  
Single Layer ◽  
Synthesis Process ◽  
Graphitic Structure ◽  
Positive Gaussian Curvature ◽  
Graphitic Sheet ◽  
Structural And Electronic Properties ◽  
New Material ◽  
Hexagonal Network

For small curvatures of a graphitic sheet, carbon atoms can maintain their preferred sp2 bonding while allowing the sheet to have various three-dimensional geometries, which may have exotic structural and electronic properties. In addition the fivefold rings will lead to a positive Gaussian curvature in the hexagonal network, and the sevenfold rings cause a negative one. By combining these sevenfold and fivefold rings with sixfold rings, it is possible to construct complicated carbon sp2 networks. Because it is much easier to introduce pentagons and heptagons into the single-layer hexagonal network than into the multilayer network, the complicated morphologies would be more common in the single-layer graphite structures. In this contribution, we report the observation and characterization of a new material of monolayer graphitic structure by electron diffraction, HREM, EELS.The synthesis process used in this study is reported early. We utilized a composite anode of graphite and copper for arc evaporation in helium.

Characterization of Monoclonal Anti-human Factor VII Antibody (B101/B1) that Recognized Three-dimensional Structures near Arg at Position 79 in the First EGF-like Domain

1998 ◽  
Vol 79 (01) ◽  
pp. 104-109 ◽  
Author(s):  
Osamu Takamiya
Keyword(s):  
Monoclonal Antibodies ◽  
Tissue Factor ◽  
Human Factor ◽  
Solid Phase ◽  
Three Dimensional ◽  
Coagulation Factors ◽  
Factor Vii ◽  
Dimensional Structure ◽  
Epidermal Growth

SummaryMurine monoclonal antibodies (designated hVII-B101/B1, hVIIDC2/D4 and hVII-DC6/3D8) directed against human factor VII (FVII) were prepared and characterized, with more extensive characterization of hVII-B101/B1 that did not bind reduced FVIIa. The immunoglobulin of the three monoclonal antibodies consisted of IgG1. These antibodies did not inhibit procoagulant activities of other vitamin K-dependent coagulation factors except FVII and did not cross-react with proteins in the immunoblotting test. hVII-DC2/D4 recognized the light chain after reduction of FVIIa with 2-mercaptoethanol, and hVIIDC6/3D8 the heavy chain. hVII-B101/B1 bound FVII without Ca2+, and possessed stronger affinity for FVII in the presence of Ca2+. The Kd for hVII-B101/B1 to FVII was 1.75 x 10–10 M in the presence of 5 mM CaCl2. The antibody inhibited the binding of FVII to tissue factor in the presence of Ca2+. hVII-B101/B1 also inhibited the activation of FX by the complex of FVIIa and tissue factor in the presence of Ca2+. Furthermore, immunoblotting revealed that hVII-B101/B1 reacted with non-reduced γ-carboxyglutaminic acid (Gla)-domainless-FVII and/or FVIIa. hVII-B101/B1 showed a similar pattern to that of non-reduced proteolytic fragments of FVII by trypsin with hVII-DC2/D4 on immunoblotting test. hVII-B101/B1 reacted differently with the FVII from the dysfunctional FVII variant, FVII Shinjo, which has a substitution of Gln for Arg at residue 79 in the first epidermal growth factor (1st EGF)-like domain (Takamiya O, et al. Haemosta 25, 89-97,1995) compared with normal FVII, when used as a solid phase-antibody for ELISA by the sandwich method. hVII-B101/B1 did not react with a series of short peptide sequences near position 79 in the first EGF-like domain on the solid-phase support for epitope scanning. These results suggested that the specific epitope of the antibody, hVII-B101/B1, was located in the three-dimensional structure near position 79 in the first EGF-like domain of human FVII.

Scanning-tunneling spectroscopy on conjugated polymer films

2003 ◽  
Vol 771 ◽  
Author(s):  
M. Kemerink ◽  
S.F. Alvarado ◽  
P.M. Koenraad ◽  
R.A.J. Janssen ◽  
H.W.M. Salemink ◽  
...  
Keyword(s):  
Polymer Films ◽  
Conjugated Polymer ◽  
Three Dimensional ◽  
Field Enhancement ◽  
Direct Consequence ◽  
Scanning Tunneling Spectroscopy ◽  
Tunneling Spectroscopy ◽  
Band Alignment ◽  
Scanning Tunneling ◽  
Order Of Magnitude

AbstractScanning-tunneling spectroscopy experiments have been performed on conjugated polymer films and have been compared to a three-dimensional numerical model for charge injection and transport. It is found that field enhancement near the tip apex leads to significant changes in the injected current, which can amount to more than an order of magnitude, and can even change the polarity of the dominant charge carrier. As a direct consequence, the single-particle band gap and band alignment of the organic material can be directly obtained from tip height-voltage (z-V) curves, provided that the tip has a sufficiently sharp apex.

Active Learning Accelerates Ab Initio Molecular Dynamics on Pericyclic Reactive Energy Surfaces

2020 ◽  
Author(s):  
Shi Jun Ang ◽  
Wujie Wang ◽  
Daniel Schwalbe-Koda ◽  
Simon Axelrod ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Transition State ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Energy Surface ◽  
Computational Cost ◽  
Reactive Trajectories ◽  
Dynamics Simulations ◽  
Energy Surfaces

<div>Modeling dynamical effects in chemical reactions, such as post-transition state bifurcation, requires <i>ab initio</i> molecular dynamics simulations due to the breakdown of simpler static models like transition state theory. However, these simulations tend to be restricted to lower-accuracy electronic structure methods and scarce sampling because of their high computational cost. Here, we report the use of statistical learning to accelerate reactive molecular dynamics simulations by combining high-throughput ab initio calculations, graph-convolution interatomic potentials and active learning. This pipeline was demonstrated on an ambimodal trispericyclic reaction involving 8,8-dicyanoheptafulvene and 6,6-dimethylfulvene. With a dataset size of approximately</div><div>31,000 M062X/def2-SVP quantum mechanical calculations, the computational cost of exploring the reactive potential energy surface was reduced by an order of magnitude. Thousands of virtually costless picosecond-long reactive trajectories suggest that post-transition state bifurcation plays a minor role for the reaction in vacuum. Furthermore, a transfer-learning strategy effectively upgraded the potential energy surface to higher</div><div>levels of theory ((SMD-)M06-2X/def2-TZVPD in vacuum and three other solvents, as well as the more accurate DLPNO-DSD-PBEP86 D3BJ/def2-TZVPD) using about 10% additional calculations for each surface. Since the larger basis set and the dynamic correlation capture intramolecular non-covalent interactions more accurately, they uncover longer lifetimes for the charge-separated intermediate on the more accurate potential energy surfaces. The character of the intermediate switches from entropic to thermodynamic upon including implicit solvation effects, with lifetimes increasing with solvent polarity. Analysis of 2,000 reactive trajectories on the chloroform PES shows a qualitative agreement with the experimentally-reported periselectivity for this reaction. This overall approach is broadly applicable and opens a door to the study of dynamical effects in larger, previously-intractable reactive systems.</div>

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