scholarly journals A novel framework for molecular characterization of atmospherically relevant organic compounds based on collision cross section and mass-to-charge ratio

2016 ◽  
Vol 16 (20) ◽  
pp. 12945-12959 ◽  
Author(s):  
Xuan Zhang ◽  
Jordan E. Krechmer ◽  
Michael Groessl ◽  
Wen Xu ◽  
Stephan Graf ◽  
...  
Keyword(s):  
Organic Compounds ◽  
Cross Section ◽  
Cross Sections ◽  
Collision Cross Section ◽  
Molecular Structures ◽  
Molecular Signature ◽  
Charge Ratio ◽  
Dynamics Simulations ◽  
Chemical Class ◽  
Atmospherically Relevant

Abstract. A new metric is introduced for representing the molecular signature of atmospherically relevant organic compounds, the collision cross section (Ω), a quantity that is related to the structure and geometry of molecules and is derived from ion mobility measurements. By combination with the mass-to-charge ratio (m∕z), a two-dimensional Ω − m∕z space is developed to facilitate the comprehensive investigation of the complex organic mixtures. A unique distribution pattern of chemical classes, characterized by functional groups including amine, alcohol, carbonyl, carboxylic acid, ester, and organic sulfate, is developed on the 2-D Ω − m∕z space. Species of the same chemical class, despite variations in the molecular structures, tend to situate as a narrow band on the space and follow a trend line. Reactions involving changes in functionalization and fragmentation can be represented by the directionalities along or across these trend lines, thus allowing for the interpretation of atmospheric transformation mechanisms of organic species. The characteristics of trend lines for a variety of functionalities that are commonly present in the atmosphere can be predicted by the core model simulations, which provide a useful tool to identify the chemical class to which an unknown species belongs on the Ω − m∕z space. Within the band produced by each chemical class on the space, molecular structural assignment can be achieved by utilizing collision-induced dissociation as well as by comparing the measured collision cross sections in the context of those obtained via molecular dynamics simulations.

scholarly journals A Novel Framework for Molecular Characterization of Atmospheric Organic Aerosol Based on Collision Cross Section and Mass-to-Charge Ratio

2016 ◽  
Author(s):  
X. Zhang ◽  
J. E. Krechmer ◽  
M. Groessl ◽  
W. Xu ◽  
S. Graf ◽  
...  
Keyword(s):  
Cross Section ◽  
Cross Sections ◽  
Collision Cross Section ◽  
Organic Aerosol ◽  
Molecular Structures ◽  
Molecular Signature ◽  
Charge Ratio ◽  
Ambient Aerosols ◽  
Dynamics Simulations ◽  
Chemical Class

Abstract. A new metric is introduced for representing the molecular signature of atmospheric organic aerosols, the collision cross section (Ω), a quantity that is related to the structure and geometry of molecules and is derived from ion mobility measurements. By combination with the mass-to-charge ratio (m/z), a two-dimensional Ω–m/z space is developed to facilitate the comprehensive investigation of the complex organic aerosol mixture. A unique distribution pattern of chemical classes, characterized by functional groups including amine, alcohol, carbonyl, carboxylic acid, ester, and organic sulfate, is developed on the 2-D Ω–m/z space. Species of the same chemical class, despite variations in the molecular structures, tend to situate as a narrow band on the space and follow a trend line. Reactions involving changes in functionalization and fragmentation can be represented by the directionalities along or across these trend lines, thus allowing for the interpretation of mechanisms associated with the formation and evolution of atmospheric organic aerosol. The characteristics of trend lines for a variety of functionalities that are commonly present in ambient aerosols can be predicted by the core model simulations, which provide a useful tool to identify the chemical class to which an unknown species belongs on the Ω–m/z space. Within the band produced by each chemical class on the space, molecular structural assignment can be achieved by utilizing collision induced dissociation as well as by comparing the measured collision cross sections in the context of those obtained via molecular dynamics simulations.

Electron energy distributions in uniform electric fields and the Townsend ionization coefficient

1958 ◽  
Vol 244 (1237) ◽  
pp. 166-185 ◽  
Keyword(s):  
Differential Equation ◽  
Cross Section ◽  
Electric Fields ◽  
Cross Sections ◽  
Collision Cross Section ◽  
Present Theory ◽  
Uniform Electric Field ◽  
Ionization Coefficient ◽  
Special Cases ◽  
Wide Range

The second-order differential equation which expresses the equilibrium condition of an electron swarm in a uniform electric field in a gas, the electrons suffering both elastic and inelastic collisions with the gas molecules, is solved by the Jeffreys or W.K.B. method of approximation. The distribution function F(ε) of electrons of energy ε is obtained immediately in a general form involving the elastic and inelastic collision cross-sections and without any restriction on the range of E/p (electric strength/gas pressure) save that introduced in the original differential equation. In almost all applications the approximation is likely to be of high accuracy, and easy to use. Several of the earlier derivations of F(ε) are obtained as special cases. Using the function F(ε) an attempt is made to relate the Townsend ionization coefficient a to the properties of the gas in a more general manner than hitherto, using realistic functions for the collision cross-section. It is finally expressed by the equation α/ p = A exp ( — Bp/E ) in which A and B are functions involving the properties of the gas and the ratio E/p . The important coefficient B is directly related to the form and magnitude of the total inelastic cross-section below the ionization potential and can be evaluated for a particular gas once the cross-section is known experimentally. The present theory shows clearly the influence of E/p on both A and B, a matter which has not been satisfactorily discussed previously. The theory is illustrated by calculations of F (ε) and a/p for hydrogen over a range of E/p from 10 to 1000. The agreement between the calculated results and recent reliable observations of α/ p is surprisingly good considering the nature of the calculations and the wide range of E/p .

Characterisation of Calmodulin Structural Transitions by Ion Mobility Mass Spectrometry

2012 ◽  
Vol 65 (5) ◽  
pp. 504 ◽  
Author(s):  
Antonio N. Calabrese ◽  
Lauren A. Speechley ◽  
Tara L. Pukala
Keyword(s):  
Mass Spectrometry ◽  
Cross Section ◽  
Cross Sections ◽  
Ion Mobility ◽  
Collision Cross Section ◽  
Travelling Wave ◽  
Ion Mobility Mass Spectrometry ◽  
Structural Transitions ◽  
Calmodulin Binding ◽  
Negative Mode

This study demonstrates the ability of travelling wave ion mobility-mass spectrometry to measure collision cross-sections of ions in the negative mode, using a calibration based approach. Here, negative mode ion mobility-mass spectrometry was utilised to understand structural transitions of calmodulin upon Ca2+ binding and complexation with model peptides melittin and the plasma membrane Ca2+ pump C20W peptide. Coexisting calmodulin conformers were distinguished on the basis of their mass and cross-section, and identified as relatively folded and unfolded populations, with good agreement in collision cross-section to known calmodulin geometries. Titration of calcium tartrate to physiologically relevant Ca2+ levels provided evidence for intermediately metalated species during the transition from apo- to holo-calmodulin, with collision cross-section measurements indicating that higher Ca2+ occupancy is correlated with more compact structures. The binding of two representative peptides which exemplify canonical compact (melittin) and extended (C20W) peptide-calmodulin binding models has also been interrogated by ion mobility mass spectrometry. Peptide binding to calmodulin involves intermediates with metalation states from 1–4 Ca2+, which demonstrate relatively collapsed structures, suggesting neither the existence of holo-calmodulin or a pre-folded calmodulin conformation is a prerequisite for binding target peptides or proteins. The biological importance of the different metal unsaturated calmodulin complexes, if any, is yet to be understood.

scholarly journals Some Recent Studies of Electron Swarms in Gases

1992 ◽  
Vol 45 (3) ◽  
pp. 365 ◽  
Author(s):  
H Tagashira
Keyword(s):  
Boltzmann Equation ◽  
Cross Section ◽  
Electric Fields ◽  
Cross Sections ◽  
Collision Cross Section ◽  
Vibrational Excitation ◽  
Time Spectrum ◽  
Electron Collision ◽  
Electron Drift ◽  
Radio Frequency Electric Fields

Some recent studies of electron swarms in gases under the action of an electric field are introduced. The studies include a new type of continuity equation for electrons having a form in which the partial derivative of the electron density with respect to position and to time are interchanged, a method to deduce the time-of-flight and arrival-time-spectrum swarm parameters based on a Fourier-transformed Boltzmann equation, an examination of the correspondence between experimental and theoretical electron drift velocities, and an automatic technique to deduce the electron-gas molecule collision cross section from electron drift velocity data. We also briefly introduce a method for the deduction of electron collision cross sections with gas molecules having vibrational excitation cross sections greater than the elastic momentum transfer cross section by using a gas mixture technique, an integral type of method for solution of the Boltzmann equation with salient numerical stability, a quantitative analysis of the effect of Penning ionisation, and the behaviour of electron swarms under radio frequency electric fields.

scholarly journals A parallelized molecular collision cross section package with optimized accuracy and efficiency

The Analyst ◽  
2019 ◽  
Vol 144 (5) ◽  
pp. 1660-1670 ◽  
Author(s):  
Christian Ieritano ◽  
Jeff Crouse ◽  
J. Larry Campbell ◽  
W. Scott Hopkins
Keyword(s):  
Cross Section ◽  
Cross Sections ◽  
Collision Cross Section ◽  
High Accuracy ◽  
Molecular Collision ◽  
Collision Cross Sections

A new parallelized calculation package predicts collision cross sections with high accuracy and efficiency.

Superoperator methods of calculating cross sections: II. Distorted wave Born approximation

1976 ◽  
Vol 54 (13) ◽  
pp. 1328-1342 ◽  
Author(s):  
R. F. Snider ◽  
R. E. Turner
Keyword(s):  
Cross Section ◽  
Cross Sections ◽  
Correlation Functions ◽  
Born Approximation ◽  
Collision Cross Section ◽  
Internal State ◽  
Time Correlation ◽  
State Transitions ◽  
Distorted Wave ◽  
Distorted Wave Born Approximation

The superoperator form of the collision cross section is evaluated within the distorted wave Born approximation. It is first verified that the obvious expansion methods give a result identical to that obtained by standard methods. Formalistically, the algebraic expansions of the transition operator and superoperator are shown to have parallel structures. The distorted wave Born approximation for the cross section also has a structure parallel to the structure of the Born approximation cross section. This is especially brought out by formulating the results in terms of time correlation functions. Certain simplifying features are found for cross sections averaged over initial and final velocity directions. These cross sections for internal state transitions are further simplified by averaging over a Maxwellian distribution of initial velocities in such a way as to obtain 'kinetic cross sections' appropriate for gas kinetic phenomena. Connection is also made with the 'constant acceleration approximation' used to estimate correlation functions in gas phase NMR.

Code Development for the Neutronics/Thermal-Hydraulics Coupling Transient Analysis of Molten Salt Reactors

2017 ◽  
Author(s):  
Tianliang Hu ◽  
Liangzhi Cao ◽  
Hongchun Wu ◽  
Kun Zhuang
Keyword(s):  
Molten Salt ◽  
Cross Section ◽  
Cross Sections ◽  
Transient Analysis ◽  
Reactor Core ◽  
Dynamics Simulation ◽  
Monte Carlo Code ◽  
Section Data ◽  
Dynamics Simulations ◽  
Data Library

A code system has been developed in this paper for the dynamics simulations of MSRs. The homogenized cross section data library is generated using the continuous-energy Monte-Carlo code OpenMC which provides significant modeling flexibility compared against the traditional deterministic lattice transport codes. The few-group cross sections generated by OpenMC are provided to TANSY and TANSY_K which is based on OpenFOAM to perform the steady-state full-core coupled simulations and dynamics simulation. For verification and application of the codes sequence, the simulation of a representative molten salt reactor core MOSART has been performed. For the further study of the characteristics of MSRs, several transients like the code-slug transient, unprotected loss of flow transient and overcooling transient have been analyzed. The numerical results indicated that the TANSY and TANSY_K codes with the cross section library generated by OpenMC has the capability for the dynamics analysis of MSRs.

scholarly journals Collision Cross Sections of Charge-Reduced Proteins and Protein Complexes: A Database for Collision Cross Section Calibration

2020 ◽  
Vol 92 (6) ◽  
pp. 4475-4483 ◽  
Author(s):  
Alyssa Q. Stiving ◽  
Benjamin J. Jones ◽  
Jakub Ujma ◽  
Kevin Giles ◽  
Vicki H. Wysocki
Keyword(s):  
Cross Section ◽  
Cross Sections ◽  
Collision Cross Section ◽  
Protein Complexes ◽  
Collision Cross Sections
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