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Title: Dynamics of Protonated Peptide Ion Collisions with Organic Surfaces: Consonance of Simulation and Experiment

Abstract

In this Perspective mass spectrometry experiments and chemical dynamics simulations are described which have explored the atomistic dynamics of protonated peptide ions, peptide-H+, colliding with organic surfaces. These studies have investigated surface-induced dissociation (SID) for which peptide-H+ fragments upon collision with the surface, peptide-H+ physisorption on the surface, soft landing (SL), and peptide-H+ reaction with the surface, reactive landing (RL). The simulations include QM+MM and QM/MM direct dynamics. For collisions with self-assembled monolayer (SAM) surfaces there is quite good agreement between experiment and simulation in the efficiency of energy transfer to the peptide-H+ ion’s internal degrees of freedom. Both the experiments and simulations show two mechanisms for peptide-H+ fragmentation, i.e. shattering and statistical, RRKM dynamics. Mechanisms for SL are probed in simulations of collisions of protonated dialanine with a perfluorinated SAM surface. RL has been studied experimentally for a number of peptide-H+ + surface systems, and qualitative agreement between simulation and experiment is found for two similar systems.

Authors:
; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1314412
Report Number(s):
PNNL-SA-117967
Journal ID: ISSN 1948-7185; KC0302020
DOE Contract Number:
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Physical Chemistry Letters; Journal Volume: 7; Journal Issue: 16
Country of Publication:
United States
Language:
English

Citation Formats

Pratihar, Subha, Barnes, George L., Laskin, Julia, and Hase, William L.. Dynamics of Protonated Peptide Ion Collisions with Organic Surfaces: Consonance of Simulation and Experiment. United States: N. p., 2016. Web. doi:10.1021/acs.jpclett.6b00978.
Pratihar, Subha, Barnes, George L., Laskin, Julia, & Hase, William L.. Dynamics of Protonated Peptide Ion Collisions with Organic Surfaces: Consonance of Simulation and Experiment. United States. doi:10.1021/acs.jpclett.6b00978.
Pratihar, Subha, Barnes, George L., Laskin, Julia, and Hase, William L.. 2016. "Dynamics of Protonated Peptide Ion Collisions with Organic Surfaces: Consonance of Simulation and Experiment". United States. doi:10.1021/acs.jpclett.6b00978.
@article{osti_1314412,
title = {Dynamics of Protonated Peptide Ion Collisions with Organic Surfaces: Consonance of Simulation and Experiment},
author = {Pratihar, Subha and Barnes, George L. and Laskin, Julia and Hase, William L.},
abstractNote = {In this Perspective mass spectrometry experiments and chemical dynamics simulations are described which have explored the atomistic dynamics of protonated peptide ions, peptide-H+, colliding with organic surfaces. These studies have investigated surface-induced dissociation (SID) for which peptide-H+ fragments upon collision with the surface, peptide-H+ physisorption on the surface, soft landing (SL), and peptide-H+ reaction with the surface, reactive landing (RL). The simulations include QM+MM and QM/MM direct dynamics. For collisions with self-assembled monolayer (SAM) surfaces there is quite good agreement between experiment and simulation in the efficiency of energy transfer to the peptide-H+ ion’s internal degrees of freedom. Both the experiments and simulations show two mechanisms for peptide-H+ fragmentation, i.e. shattering and statistical, RRKM dynamics. Mechanisms for SL are probed in simulations of collisions of protonated dialanine with a perfluorinated SAM surface. RL has been studied experimentally for a number of peptide-H+ + surface systems, and qualitative agreement between simulation and experiment is found for two similar systems.},
doi = {10.1021/acs.jpclett.6b00978},
journal = {Journal of Physical Chemistry Letters},
number = 16,
volume = 7,
place = {United States},
year = 2016,
month = 8
}
  • Chemical dynamics simulations are reported which provide atomistic details of collisions of protonated dialanine, ala2-H+, with a perfluorinateted octanethiolate self-assembled monolayer (F-SAM ) surface. The simulations are performed at collisions energy Ei of 5.0, 13.5, 22.5, 30.00, and 70 eV, and incident angles 0o 0 (normal) and grazing 45o. Excellent agreement with experiment (J. Am. Chem. Soc. 2000, 122, 9703-9714) is found for both the average fraction and distribution of the collision energy transferred to the ala2-H+ internal degrees of freedom. The dominant pathway for this energy transfer is to ala2-H+ vibration, but for Ei = 5.0 eV ~20% ofmore » the energy transfer is to ala2-H+ rotation. Energy transfer to ala2-H+ rotation decreases with increase in Ei and becomes negligible at high Ei. Three types of collisions are observed in the simulations: i.e. those for which ala2-H+ (1) directly scatters off the F-SAM surface; (2) sticks/physisorbs on//in the surface, but desorbs within the 10 ps numerical integration of the simulations; and (3) remains trapped (i.e. soft-landed) on/in the surface when the simulations are terminated. Penetration of the F-SAM by ala2-H+ is important for the latter two types of events. The trapped trajectories are expected to have relatively long residence times on the surface, since a previous molecular dynamics simulation (J. Phys. Chem. B 2014, 118, 5577-5588) shows that thermally accommodated ala2-H+ ions have an binding energy with the F-SAM surface of at least ~15 kcal/mol.« less
  • Direct dynamics simulations are reported for quantum mechanical (QM)/molecular mechanical (MM) trajectories of N-protonated diglycine (gly{sub 2}-H{sup +}) colliding with chemically modified perfluorinated octanethiolate self-assembled monolayer (SAM) surfaces. The RM1 semiempirical theory is used for the QM component of the trajectories. RM1 activation and reaction energies were compared with those determined from higher-level ab initio theories. Two chemical modifications are considered in which a head group (-COCl or -CHO) is substituted on the terminal carbon of a single chain of the SAM. These surfaces are designated as the COCl-SAM and CHO-SAM, respectively. Fragmentation, peptide reaction with the SAM, and covalentmore » linkage of the peptide or its fragments with the SAM surface are observed. Peptide fragmentation via concerted CH{sub 2}-CO bond breakage is the dominant pathway for both surfaces. HCl formation is the dominant species produced by reaction with the COCl-SAM, while for the CHO-SAM a concerted H-atom transfer from the CHO-SAM to the peptide combined with either a H-atom or radical transfer from the peptide to the surface to form singlet reaction products is the dominant pathway. A strong collision energy dependence is found for the probability of peptide fragmentation, its reactivity, and linkage with the SAM. Surface deposition, i.e., covalent linkage between the surface and the peptide, is compared to recent experimental observations of such bonding by Laskin and co-workers [Phys. Chem. Chem. Phys. 10, 1512 (2008)]. Qualitative differences in reactivity are seen between the COCl-SAM and CHO-SAM showing that chemical identity is important for surface reactivity. The probability of reactive surface deposition, which is most closely analogous to experimental observables, peaks at a value of around 20% for a collision energy of 50 eV.« less
  • Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible syntheticmore » polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in β-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended β-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form β turns or α helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit solvent, we performed in this work the classical molecular dynamics simulation on a realistic model solution with the peptide embedded in an explicit water environment, and calculated its dynamic properties both as an outcome of the simulations, and by the diffusion theory in reduced statistical-mechanical approach within HBA on the premise that the mode-coupling approach to the diffusion theory can give both the long-range and local dynamics starting from equilibrium averages which were obtained from detailed atomistic simulations.« less
  • Time- and energy-resolved surface induced (SID) dissociation of a singly protonated octapeptide des-Arg1-bradykinin (PPGFSPFR) was used to study the effect of physical properties of the SID target on the efficiency of translational to vibrational energy transfer (T > V) in collisions of peptide ions with surfaces. Four SID targets of varying chemical composition and stiffness were examined in this work: self-assembled monolayers of 1-dodecane thiol (HSAM) and its fluorinated analog (CF3(CF2)9C2H4SH - FSAM) on gold, a 300 nm thick layer of lithium fluoride (LiF) on a polished titanium surface, and a 2 m carbon vapor deposited diamond layer on amore » titanium surface. An RRKM-based modeling approach was utilized to extract internal energy distributions deposited into the precursor ion upon collisions with different surfaces. We found that the percent of T -> V transfer increases in the order: HSAM (10.1%), LiF (12.0%), diamond (19.2%), FSAM (20.5%). Furthermore, the width of the energy deposition function (EDF) is affected by the properties of the SID target. Collisions of peptide ions with the HSAM surface results in deposition of relatively narrow internal energy distributions with the width of the EDF increasing in the order: HSAM < FSAM < LiF < Diamond. The results demonstrate that surface stiffness has a major effect on the width of the EDF, while the average energy deposited into the ion is mainly affected by the mass of the chemical moiety representing an immediate collision partner for the ion impacting the surface.« less
  • The gas phase photodissociation spectra of benzoyl cation, protonated benzene, and protonated mesitylene are reported and compared to their solution absorption spectra. Each ion exhibits two maxima in the wavelength region 2000--4000 A. The values of lambda/sub max/ for the benzoyl cation (C/sub 6/H/sub 5/CO/sup +/ + h..nu.. ..-->.. C/sub 6/H/sub 5//sup +/ + CO) are 260 +- 10 nm (sigma approximately equal to 0.15 A/sup 2/) and 310 +- 10 nm (sigma approximately equal to 0.04 A/sup 2/), for protonated benzene (C/sub 6/H/sub 7//sup +/ + h..nu.. ..-->.. C/sub 6/H/sub 5//sup +/ + H/sub 2/) 245 +- 10 nmmore » (sigma approximately equal to 0.02 A) and 330 +- 10 nm (sigma approximately equal to 0.08 A/sup 2/), and for protonated mesitylene (C/sub 9/H/sub 13//sup +/ + h..nu.. ..-->.. products) 250 +- 10 nm (sigma approximately equal to 0.06 A/sup 2/) and 355 +- 10 nm (sigma approximately equal to 0.10 A/sup 2/). With the exception of protonated benzene, excellent agreement between the solution absorption spectra and gas phase photodissociation spectra is observed. The lack of agreement for protonated benzene is attributed to other absorbing species present in solution. From a comparison of the gas phase and solution spectra, it can be inferred that the quantum yields for photodissociation do not vary significantly with wavelength and are thus very likely close to unity. In addition, there is no detectable solvent shift for any of the observed transitions.« less