Radiative double electron capture (RDEC), occurring when two electrons are captured to a projectile ion with the simultaneous emission of a single photon, has been investigated. RDEC can be considered as the time inverse process of double photoionization. Strong evidence for RDEC is found in F9++ N2collisions and additionally for one‐electron F8+for which the probability for the process is expected to be considerably smaller. Preliminary values for the cross sections for RDEC have been determined. A significant advantage of the gas target is that multiple‐collision effects seen for a solid target are avoided due to the single‐collision conditions that prevail for gas targets.
Single and double electron capture associated with target K‐shell ionization for F 7 + ,8 + ,9+ +Ar
Ratios for target Ar K‐shell ionization associated with single and double electron capture, as well as the ratios corresponding to total capture and the projectile K x rays, were determined for 1.8‐ to 2.2‐MeV/u F7 + ,8 + ,9+projectiles. This work was performed at Western Michigan University with the tandem Van de Graaff accelerator. Coincidences between emitted K‐shell X‐rays (both target and projectile) and the corresponding charge‐changed particles were observed. The F9+Ar K X‐ray coincidence ratios for double to single capture are found to well exceed unity over the limited energy range of the measurements. Possible explanations for this anomalous behavior are discussed.
more » « less- Award ID(s):
- 1707467
- NSF-PAR ID:
- 10453926
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- X-Ray Spectrometry
- Volume:
- 49
- Issue:
- 1
- ISSN:
- 0049-8246
- Page Range / eLocation ID:
- p. 60-64
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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null (Ed.)We have measured differential yields for double capture and double capture accompanied by ionization in 75 keV p + Ar collisions. Data were taken for two different transverse projectile coherence lengths. A small effect of the projectile coherence properties on the yields were found for double capture, but not for double capture plus ionization. The results suggest that multiple projectile–target interactions can lead to a significant weakening of projectile coherence effects.more » « less
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Abstract The millimeter-wave spectrum of the SiP radical (X2Πi) has been measured in the laboratory for the first time using direct-absorption methods. SiP was created by the reaction of phosphorus vapor and SiH4in argon in an AC discharge. Fifteen rotational transitions (
J + 1 ←J ) were measured for SiP in the Ω = 3/2 ladder in the frequency range 151–533 GHz, and rotational, lambda doubling, and phosphorus hyperfine constants determined. Based on the laboratory measurements, SiP was detected in the circumstellar shell of IRC+10216, using the Submillimeter Telescope and the 12 m antenna of the Arizona Radio Observatory at 1 mm and 2 mm, respectively. Eight transitions of SiP were searched: four were completely obscured by stronger features, two were uncontaminated (J = 13.5 → 12.5 and 16.5 → 15.5), and two were partially blended with other lines (J = 8.5 → 7.5 and 17.5 → 16.5). The SiP line profiles were broader than expected for IRC+10216, consistent with the hyperfine splitting. From non-LTE radiative transfer modeling, SiP was found to have a shell distribution with a radius ∼300R *, and an abundance, relative to H2, off ∼ 2 × 10−9. From additional modeling, abundances of 7 × 10−9and 9 × 10−10were determined for CP and PN, respectively, both located in shells at 550–650R *. SiP may be formed from grain destruction, which liberates both phosphorus and silicon into the gas phase, and then is channeled into other P-bearing molecules such as PN and CP. -
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Abstract We report relatively persistent, open‐shell thiophene‐based double helices, radical cations 1•+‐TMS12and 2•+‐TMS8. Closed‐shell neutral double helices, 1‐TMS12and 2‐TMS8, have nearly identical first oxidation potentials,
E +/0 ≈ +1.33 V, corresponding to reversible oxidation to their radical cations. The radical cations are generated, using tungsten hexachloride in dichloromethane (DCM) as an oxidant,E +/0 ≈ +1.56 V. EPR spectra consist of a relatively sharp singlet peak with an unusually lowg ‐value of 2.001–2.002, thus suggesting exclusive delocalization of spin density over π‐conjugated system consisting of carbon atoms only. DFT computations confirm these findings, as only negligible fraction of spin density is found on sulfur and silicon atoms and the spin density is delocalized over a single tetrathiophene moiety. For radical cation, 1•+‐TMS12, energy level of the singly occupied molecular orbital (SOMO) lies below the four highest occupied molecular orbitals (HOMOs), thus indicating the SOMO–HOMO inversion (SHI) and therefore, violating the Aufbau principle. 1•+‐TMS12has a half‐life of the order of only 5 min at room temperature. EPR peak intensity of 2•+‐TMS8, which does not show SHI, is practically unchanged over at least 2 h. -
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This data set for the manuscript entitled "Design of Peptides that Fold and Self-Assemble on Graphite" includes all files needed to run and analyze the simulations described in the this manuscript in the molecular dynamics software NAMD, as well as the output of the simulations. The files are organized into directories corresponding to the figures of the main text and supporting information. They include molecular model structure files (NAMD psf or Amber prmtop format), force field parameter files (in CHARMM format), initial atomic coordinates (pdb format), NAMD configuration files, Colvars configuration files, NAMD log files, and NAMD output including restart files (in binary NAMD format) and trajectories in dcd format (downsampled to 10 ns per frame). Analysis is controlled by shell scripts (Bash-compatible) that call VMD Tcl scripts or python scripts. These scripts and their output are also included.
Version: 2.0
Changes versus version 1.0 are the addition of the free energy of folding, adsorption, and pairing calculations (Sim_Figure-7) and shifting of the figure numbers to accommodate this addition.
Conventions Used in These Files
===============================Structure Files
----------------
- graph_*.psf or sol_*.psf (original NAMD (XPLOR?) format psf file including atom details (type, charge, mass), as well as definitions of bonds, angles, dihedrals, and impropers for each dipeptide.)- graph_*.pdb or sol_*.pdb (initial coordinates before equilibration)
- repart_*.psf (same as the above psf files, but the masses of non-water hydrogen atoms have been repartitioned by VMD script repartitionMass.tcl)
- freeTop_*.pdb (same as the above pdb files, but the carbons of the lower graphene layer have been placed at a single z value and marked for restraints in NAMD)
- amber_*.prmtop (combined topology and parameter files for Amber force field simulations)
- repart_amber_*.prmtop (same as the above prmtop files, but the masses of non-water hydrogen atoms have been repartitioned by ParmEd)Force Field Parameters
----------------------
CHARMM format parameter files:
- par_all36m_prot.prm (CHARMM36m FF for proteins)
- par_all36_cgenff_no_nbfix.prm (CGenFF v4.4 for graphene) The NBFIX parameters are commented out since they are only needed for aromatic halogens and we use only the CG2R61 type for graphene.
- toppar_water_ions_prot_cgenff.str (CHARMM water and ions with NBFIX parameters needed for protein and CGenFF included and others commented out)Template NAMD Configuration Files
---------------------------------
These contain the most commonly used simulation parameters. They are called by the other NAMD configuration files (which are in the namd/ subdirectory):
- template_min.namd (minimization)
- template_eq.namd (NPT equilibration with lower graphene fixed)
- template_abf.namd (for adaptive biasing force)Minimization
-------------
- namd/min_*.0.namdEquilibration
-------------
- namd/eq_*.0.namdAdaptive biasing force calculations
-----------------------------------
- namd/eabfZRest7_graph_chp1404.0.namd
- namd/eabfZRest7_graph_chp1404.1.namd (continuation of eabfZRest7_graph_chp1404.0.namd)Log Files
---------
For each NAMD configuration file given in the last two sections, there is a log file with the same prefix, which gives the text output of NAMD. For instance, the output of namd/eabfZRest7_graph_chp1404.0.namd is eabfZRest7_graph_chp1404.0.log.Simulation Output
-----------------
The simulation output files (which match the names of the NAMD configuration files) are in the output/ directory. Files with the extensions .coor, .vel, and .xsc are coordinates in NAMD binary format, velocities in NAMD binary format, and extended system information (including cell size) in text format. Files with the extension .dcd give the trajectory of the atomic coorinates over time (and also include system cell information). Due to storage limitations, large DCD files have been omitted or replaced with new DCD files having the prefix stride50_ including only every 50 frames. The time between frames in these files is 50 * 50000 steps/frame * 4 fs/step = 10 ns. The system cell trajectory is also included for the NPT runs are output/eq_*.xst.Scripts
-------
Files with the .sh extension can be found throughout. These usually provide the highest level control for submission of simulations and analysis. Look to these as a guide to what is happening. If there are scripts with step1_*.sh and step2_*.sh, they are intended to be run in order, with step1_*.sh first.
CONTENTS
========The directory contents are as follows. The directories Sim_Figure-1 and Sim_Figure-8 include README.txt files that describe the files and naming conventions used throughout this data set.
Sim_Figure-1: Simulations of N-acetylated C-amidated amino acids (Ac-X-NHMe) at the graphite–water interface.
Sim_Figure-2: Simulations of different peptide designs (including acyclic, disulfide cyclized, and N-to-C cyclized) at the graphite–water interface.
Sim_Figure-3: MM-GBSA calculations of different peptide sequences for a folded conformation and 5 misfolded/unfolded conformations.
Sim_Figure-4: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 370 K.
Sim_Figure-5: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 295 K.
Sim_Figure-5_replica: Temperature replica exchange molecular dynamics simulations for the peptide cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) with 20 replicas for temperatures from 295 to 454 K.
Sim_Figure-6: Simulation of the peptide molecule cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) in free solution (no graphite).
Sim_Figure-7: Free energy calculations for folding, adsorption, and pairing for the peptide CHP1404 (sequence: cyc(GTGSGTG-GPGG-GCGTGTG-SGPG)). For folding, we calculate the PMF as function of RMSD by replica-exchange umbrella sampling (in the subdirectory Folding_CHP1404_Graphene/). We make the same calculation in solution, which required 3 seperate replica-exchange umbrella sampling calculations (in the subdirectory Folding_CHP1404_Solution/). Both PMF of RMSD calculations for the scrambled peptide are in Folding_scram1404/. For adsorption, calculation of the PMF for the orientational restraints and the calculation of the PMF along z (the distance between the graphene sheet and the center of mass of the peptide) are in Adsorption_CHP1404/ and Adsorption_scram1404/. The actual calculation of the free energy is done by a shell script ("doRestraintEnergyError.sh") in the 1_free_energy/ subsubdirectory. Processing of the PMFs must be done first in the 0_pmf/ subsubdirectory. Finally, files for free energy calculations of pair formation for CHP1404 are found in the Pair/ subdirectory.
Sim_Figure-8: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) where the peptides are far above the graphene–water interface in the initial configuration.
Sim_Figure-9: Two replicates of a simulation of nine peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 370 K.
Sim_Figure-9_scrambled: Two replicates of a simulation of nine peptide molecules with the control sequence cyc(GGTPTTGGGGGGSGGPSGTGGC) at the graphite–water interface at 370 K.
Sim_Figure-10: Adaptive biasing for calculation of the free energy of the folded peptide as a function of the angle between its long axis and the zigzag directions of the underlying graphene sheet.
This material is based upon work supported by the US National Science Foundation under grant no. DMR-1945589. A majority of the computing for this project was performed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CHE-1726332, CNS-1006860, EPS-1006860, and EPS-0919443. This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1548562, through allocation BIO200030.
