1
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Bertolini S, Delcorte A. Molecular Dynamics Simulations of Soft and Reactive Landing of Proteins Desorbed by Argon Cluster Bombardment. J Phys Chem B 2024; 128:6716-6729. [PMID: 38975731 DOI: 10.1021/acs.jpcb.4c01698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Reactive molecular dynamics (MD) simulations were conducted to investigate the soft and reactive landing of hyperthermal velocity proteins transferred to a vacuum using large argon clusters. Experimentally, the interaction of argon cluster ion beams (Ar1000-5000+) with a target biofilm was previously used in such a manner to transfer lysozymes onto a collector with the retention of their bioactivity, paving the way to a new solvent-free method for complex biosurface nanofabrication. However, the experiments did not give access to a microscopic view of the interactions needed for their full understanding, which can be provided by the MD model. Our reactive force field simulations clarify the landing mechanisms of the lysozymes and their fragments on collectors with different natures (gold- and hydrogen-terminated graphite). The results highlight the conditions of soft and reactive landing on rigid surfaces, the effects of the protein structure, energy, and incidence angle before landing, and the adhesion forces with the collector substrate. Many of the obtained results can be generalized to other soft and reactive landing approaches used for biomolecules such as electrospray ionization and matrix-assisted laser desorption ionization.
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Affiliation(s)
- Samuel Bertolini
- Institute of Condensed Matter and Nanoscience, Université catholique de Louvain, 1 Place Louis Pasteur, 1348 Louvain-la-Neuve, Belgium
| | - Arnaud Delcorte
- Institute of Condensed Matter and Nanoscience, Université catholique de Louvain, 1 Place Louis Pasteur, 1348 Louvain-la-Neuve, Belgium
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2
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Frański R. Teaching mass spectrometry: A compilation of approaches to teaching theory and practice of mass spectrometry. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2024; 30:87-102. [PMID: 38444356 DOI: 10.1177/14690667241237431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
The areas of mass spectrometry applications seem to be much larger than those of any other analytical techniques. They extend from the determination of molecular mass in organic chemistry, through the analytical applications in forensic, environmental and omics sciences, the application in extra-terrestrial exploration and many others. Mass spectrometry, usually coupled with chromatographic techniques, has also found wide application in the pharmaceutical industry, forensic laboratories, laboratories of sanitary inspection or environmental inspection, etc. The growing areas of applications give rise to the demand for the comprehensive mass spectrometry education of undergraduates. This overview covers the body of literature describing various interesting ideas that can be successfully used for teaching mass spectrometry. Since mass spectrometry is a multidisciplinary field, old but dynamically developing, teaching mass spectrometry may be more problematic in comparison to teaching other analytical techniques, for example, there is the problem of position of mass spectrometry in the chemistry curriculum. On the other hand, it is obvious that the mass spectrometry community, besides difficult scientific work, does great and admirable teaching work, in order to perfectly educate undergraduates in the field of mass spectrometry and to make learning mass spectrometry as attractive as possible.
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Affiliation(s)
- Rafał Frański
- Faculty of Chemistry, Adam Mickiewicz University, Poznań, Poland
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3
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Louerdi S, Hrabar S, Mouhib T, Kański M, Postawa Z. Ar cluster bombardment of phenylalanine deposited on graphene-Effect of kinetic energy and projectile size. J Chem Phys 2023; 159:204705. [PMID: 38010336 DOI: 10.1063/5.0169830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/31/2023] [Indexed: 11/29/2023] Open
Abstract
This study investigates the effects of kinetic energy and projectile size on particle emission from a phenylalanine overlayer adsorbed on a graphene bilayer during argon projectile bombardment. Projectiles of various sizes (1-1000 atoms) and kinetic energies (0.5-40 keV) are used to study their impact on the ejection efficiency, mass distribution, and kinetic and angular spectra of the emitted substances. Particle ejection mechanisms are discussed in scenarios with and without sample perforation. Additionally, this study investigated the potential use of graphene in secondary ion mass spectrometry or neutral secondary mass spectrometry analyses.
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Affiliation(s)
- Soukaina Louerdi
- LISA Laboratory, Ecole Nationale des Sciences Appliquées, Hassan First University of Settat, BP: 218, 26103 Berrechid, Morocco
| | - Sviatoslav Hrabar
- Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Lojasiewicza 11, 30-348 Kraków, Poland
| | - Taoufiq Mouhib
- LISA Laboratory, Ecole Nationale des Sciences Appliquées, Hassan First University of Settat, BP: 218, 26103 Berrechid, Morocco
| | - Michał Kański
- Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Lojasiewicza 11, 30-348 Kraków, Poland
| | - Zbigniew Postawa
- Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Lojasiewicza 11, 30-348 Kraków, Poland
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4
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Schneider P, Verloh F, Dürr M. Cluster-Induced Desorption/Ionization of Polystyrene: Desorption Mechanism and Effect of Polymer Chain Length on Desorption Probability. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:832-839. [PMID: 35426303 DOI: 10.1021/jasms.2c00021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Soft cluster-induced desorption/ionization of polystyrene oligomers was investigated with respect to application in mass spectrometry. Clear peak progressions corresponding to intact polystyrene molecules were observed in the mass spectra, and no fragmentation was detected; efficient desorption was deduced from quartz crystal microbalance measurements. Molecular dynamics (MD) simulations of the process revealed that even in the case of the nonpolar polystyrene molecules cluster-induced desorption proceeds via dissolvation in the polar clusters. Experimentally, a significantly lower desorption efficiency was observed for polystyrene molecules with larger chain length. Taking into account MD simulations and further experiments with mixed samples consisting of long- and short-chain polystyrene oligomers, the reduced desorption efficiency for longer chain polystyrene molecules was attributed to a stronger entanglement of the larger polystyrene molecules.
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Affiliation(s)
- Pascal Schneider
- Institut für Angewandte Physik and Zentrum für Materialforschung, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 16, D-35392 Giessen, Germany
| | - Felix Verloh
- Institut für Angewandte Physik and Zentrum für Materialforschung, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 16, D-35392 Giessen, Germany
| | - Michael Dürr
- Institut für Angewandte Physik and Zentrum für Materialforschung, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 16, D-35392 Giessen, Germany
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5
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Cumpson PJ, Jaskiewicz M, Kim WK. Argon cluster‐ion sputter yield: Molecular dynamics simulations on silicon and equation for estimating total sputter yield. SURF INTERFACE ANAL 2021. [DOI: 10.1002/sia.6996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Peter J. Cumpson
- NEXUS laboratory, School of Engineering Newcastle University Newcastle upon Tyne UK
- Now at Mark Wainwright Analytical Centre University of New South Wales Sydney New South Wales Australia
| | - Mieszko Jaskiewicz
- NEXUS laboratory, School of Engineering Newcastle University Newcastle upon Tyne UK
| | - Woo Kyun Kim
- Department of Mechanical and Materials Engineering University of Cincinnati Cincinnati Ohio USA
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6
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Delcorte A, Delmez V, Dupont-Gillain C, Lauzin C, Jefford H, Chundak M, Poleunis C, Moshkunov K. Large cluster ions: soft local probes and tools for organic and bio surfaces. Phys Chem Chem Phys 2020; 22:17427-17447. [PMID: 32568320 DOI: 10.1039/d0cp02398a] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Ionised cluster beams have been produced and employed for thin film deposition and surface processing for half a century. In the last two decades, kiloelectronvolt cluster ions have also proved to be outstanding for surface characterisation by secondary ion mass spectrometry (SIMS), because their sputter and ion yields are enhanced in a non-linear fashion with respect to monoatomic projectiles, with a resulting step change of sensitivity for analysis and imaging. In particular, large gas cluster ion beams, or GCIB, have now become a reference in organic surface and thin film analysis using SIMS and X-ray photoelectron spectroscopy (XPS). The reason is that they induce soft molecular desorption and offer the opportunity to conduct damageless depth-profiling and 3D molecular imaging of the most sensitive organic electronics and biological samples, with a nanoscale depth resolution. In line with these recent developments, the present review focuses on rather weakly-bound, light-element cluster ions, such as noble or other gas clusters, and water or alcohol nanodroplets (excluding clusters made of metals, inorganic salts or ionic liquids) and their interaction with surfaces (essentially, but not exclusively, organic). The scope of this article encompasses three aspects. The first one is the fundamentals of large cluster impacts with surfaces, using the wealth of information provided by molecular dynamics simulations and experimental observations. The second focus is on recent applications of large cluster ion beams in surface characterisation, including mass spectrometric analysis and 2D localisation of large molecules, molecular depth-profiling and 3D molecular imaging. Finally, the perspective explores cutting edge developments, involving (i) new types of clusters with a chemistry designed to enhance performance for mass spectrometry imaging, (ii) the use of cluster fragment ion backscattering to locally retrieve physical surface properties and (iii) the fabrication of new biosurface and thin film architectures, where large cluster ion beams are used as tools to transfer biomolecules in vacuo from a target reservoir to any collector substrate.
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Affiliation(s)
- Arnaud Delcorte
- Université Catholique de Louvain, Institute of Condensed Matter and Nanoscience, 1 Place Louis Pasteur, 1348 Louvain-la-Neuve, Belgium.
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7
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Macia̧żek D, Kański M, Postawa Z. Intuitive Model of Surface Modification Induced by Cluster Ion Beams. Anal Chem 2020; 92:7349-7353. [PMID: 32314909 PMCID: PMC7588020 DOI: 10.1021/acs.analchem.0c01219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 04/21/2020] [Indexed: 11/29/2022]
Abstract
Topography development is one of the main factors limiting the quality of depth profiles during depth profiling experiments. One possible source of topography development is the formation of self-organized patterns due to cluster ion beam irradiation. In this work, we propose a simple model that can intuitively explain this phenomenon in terms of impact-induced mass transfer. By coupling our model with molecular dynamics simulations, we can predict the critical incidence angle, which separates the smoothening and roughening regimes. The results are in quantitative agreement with experiments. It is observed that the problems arising from topography development during depth profiling with cluster projectiles can be mitigated by reducing the beam incidence angle with respect to the surface normal or increasing its kinetic energy.
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Affiliation(s)
- Dawid Macia̧żek
- Smoluchowski Institute of
Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
| | - Micha Kański
- Smoluchowski Institute of
Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
| | - Zbigniew Postawa
- Smoluchowski Institute of
Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
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8
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Schneider P, Dürr M. Cluster-induced desorption investigated by means of molecular dynamics simulations-Microsolvation in clusters of polar and non-polar constituents. J Chem Phys 2019; 150:214301. [PMID: 31176317 DOI: 10.1063/1.5095512] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The desorption of surface-adsorbed molecules induced by cluster-surface collisions of neutral molecular clusters, in particular, SO2 clusters, was investigated by means of molecular dynamics simulations. The desorption efficiency was found to be in general much higher for clusters of polar molecules when compared to nonpolar cluster constituents, for both nonpolar and polar adsorbates. In all cases, desorption is shown to proceed via dissolvation of the analyte in the cluster. In systems with nonpolar cluster constituents, the process is mainly driven by the increase in the entropy of the dissolved analyte in a larger cluster fragment. The latter process is enhanced by polar cluster constituents since the respective clusters show lower fragmentation at comparable kinetic energy and thus provide in average larger cluster fragments for the analytes to be dissolved in. In systems with clusters of polar constituents and polar adsorbates, the process is most efficient due to the additional energetic stabilization of the desorbed molecule in the solvation shell formed in the cluster fragment.
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Affiliation(s)
- P Schneider
- Institut für Angewandte Physik, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 16, D-35392 Giessen, Germany
| | - M Dürr
- Institut für Angewandte Physik, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 16, D-35392 Giessen, Germany
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9
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Abstract
The aggregation of amyloid fibrils can lead to various diseases including Alzheimer's, Parkinson's disease, and transmissible spongiform encephalopathy. Amyloid fibrils can develop from a variety of proteins in the body as they misfold into a primarily β-sheet structure and aggregate. Human lysozyme has been shown to have far reaching effects in the human health-a homologous enzyme, hen egg-white lysozyme, has been shown to denature to a primarily β-sheet structure at low pH and high alcohol content solution. We have studied these systems in atomic-level detail with a combination of constant pH and microsecond long molecular dynamics simulation in explicit solvent, which cumulatively total over 10 μs of simulation time. These studies have allowed us to determine two potential unfolding pathways depending on the protonation state of a key glutamic acid residue as well as the effect of solution dynamics and pH on the unfolding process.
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Affiliation(s)
- Alice R. Walker
- Department of Chemistry, University of North Texas, Denton, TX 76201, USA
| | - Nikhil Baddam
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - G. Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, TX 76201, USA
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10
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Tian H, Maciążek D, Postawa Z, Garrison BJ, Winograd N. C-O Bond Dissociation and Induced Chemical Ionization Using High Energy (CO 2) n+ Gas Cluster Ion Beam. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:476-481. [PMID: 30430438 PMCID: PMC6417932 DOI: 10.1007/s13361-018-2102-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 06/09/2023]
Abstract
A gas cluster ion beam (GCIB) source, consisting of CO2 clusters and operating with kinetic energies of up to 60 keV, has been developed for the high resolution and high sensitivity imaging of intact biomolecules. The CO2 molecule is an excellent molecule to employ in a GCIB source due to its relative stability and improved focusing capabilities, especially when compared to the conventionally employed Ar cluster source. Here we report on experiments aimed to examine the behavior of CO2 clusters as they impact a surface under a variety of conditions. Clusters of (CO2)n+ (n = 2000~10,000) with varying sizes and kinetic energies were employed to interrogate both an organic and inorganic surface. The results show that C-O bond dissociation did not occur when the energy per molecule is less than 5 eV/n, but that oxygen adducts were seen in increasing intensity as the energy is above 5 eV/n, particularly, drastic enhancement up to 100 times of oxygen adducts was observed on Au surface. For Irganox 1010, an organic surface, oxygen containing adducts were observed with moderate signal enhancement. Molecular dynamics computer simulations were employed to test the hypothesis that the C-O bond is broken at high values of eV/n. These calculations show that C-O bond dissociation occurs at eV/n values less than the C-O bond energy (8.3 eV) by interaction with surface topological features. In general, the experiments suggest that the projectiles containing oxygen can enhance the ionization efficiency of surface molecules via chemically induced processes, and that CO2 can be an effective cluster ion source for SIMS experiments. Graphical Abstract.
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Affiliation(s)
- Hua Tian
- Chemistry Department, The Pennsylvania State University, 215 Chemistry Building, University Park, PA, 16802, USA.
| | - Dawid Maciążek
- Smoluchowski Institute of Physics, Jagiellonian University, ulica Lojasiewicza 11, 30-348, Krakow, Poland
| | - Zbigniew Postawa
- Smoluchowski Institute of Physics, Jagiellonian University, ulica Lojasiewicza 11, 30-348, Krakow, Poland
| | - Barbara J Garrison
- Chemistry Department, The Pennsylvania State University, 215 Chemistry Building, University Park, PA, 16802, USA
| | - Nicholas Winograd
- Chemistry Department, The Pennsylvania State University, 215 Chemistry Building, University Park, PA, 16802, USA
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11
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Kański M, Maciążek D, Postawa Z, Ashraf CM, van Duin ACT, Garrison BJ. Development of a Charge-Implicit ReaxFF Potential for Hydrocarbon Systems. J Phys Chem Lett 2018; 9:359-363. [PMID: 29291618 DOI: 10.1021/acs.jpclett.7b03155] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Molecular dynamics (MD) simulations continue to make important contributions to understanding chemical and physical processes. Concomitant with the growth of MD simulations is the need to have interaction potentials that both represent the chemistry of the system and are computationally efficient. We propose a modification to the ReaxFF potential for carbon and hydrogen that eliminates the time-consuming charge equilibration, eliminates the acknowledged flaws of the electronegativity equalization method, includes an expanded training set for condensed phases, has a repulsive wall for simulations of energetic particle bombardment, and is compatible with the LAMMPS code. This charge-implicit ReaxFF potential is five times faster than the conventional ReaxFF potential for a simulation of keV particle bombardment with a sample size of over 800 000 atoms.
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Affiliation(s)
- Michał Kański
- Smoluchowski Institute of Physics, Jagiellonian University , ul. Lojasiewicza 11, 30-348 Krakow, Poland
| | - Dawid Maciążek
- Smoluchowski Institute of Physics, Jagiellonian University , ul. Lojasiewicza 11, 30-348 Krakow, Poland
| | - Zbigniew Postawa
- Smoluchowski Institute of Physics, Jagiellonian University , ul. Lojasiewicza 11, 30-348 Krakow, Poland
| | - Chowdhury M Ashraf
- Department of Mechanical and Nuclear Engineering, Penn State University , University Park, Pennsylvania 16802, United States
| | - Adri C T van Duin
- Department of Mechanical and Nuclear Engineering, Penn State University , University Park, Pennsylvania 16802, United States
| | - Barbara J Garrison
- Department of Chemistry, Penn State University , 104 Chemistry Building, University Park, Pennsylvania 16802, United States
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12
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Verkhoturov SV, Czerwinski B, Verkhoturov DS, Geng S, Delcorte A, Schweikert EA. Ejection-ionization of molecules from free standing graphene. J Chem Phys 2017; 146:084308. [PMID: 28249462 DOI: 10.1063/1.4976832] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
We present the first data on emission of C60- stimulated by single impacts of 50 keV C602+ on the self-assembled molecular layer of C60 deposited on free standing 2 layer graphene. The yield, Y, of C60- emitted in the transmission direction is 1.7%. To characterize the ejection and ionization of molecules, we have measured the emission of C60- from the surface of bulk C60 (Y = 3.7%) and from a single layer of C60 deposited on bulk pyrolytic graphite (Y = 3.3%). To gain insight into the mechanism(s) of ejection, molecular dynamic simulations were performed. The scenario of the energy deposition and ejection of molecules is different for the case of graphene due to the confined volume of projectile-analyte interaction. In the case of 50 keV C602+ impacts on graphene plus C60, the C atoms of the projectile collide with those of the target. The knocked-on atoms take on a part of the kinetic energy of the projectile atoms. Another part of the kinetic energy is deposited into the rim around the impact site. The ejection of molecules from the rim is a result of collective movement of the molecules and graphene membrane, where the membrane movement provides the impulse for ejection. The efficient emission of the intact molecular ions implies an effective ionization probability of intact C60. The proposed mechanism of ionization involves the tunneling of electrons from the vibrationally exited area around the hole to the ejecta.
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Affiliation(s)
| | - Bartlomiej Czerwinski
- Applied Physics, Division of Materials Science, Department of Engineering Sciences and Mathematics, Luleå University of Technology, SE-971 87 Luleå, Sweden
| | - Dmitriy S Verkhoturov
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3144, USA
| | - Sheng Geng
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3144, USA
| | - Arnaud Delcorte
- Institute of Condensed Matter and Nanosciences - Bio and Soft Matter (IMCN/BSMA), Université Catholique de Louvain, 1 Croix du Sud, B-1348 Louvain-la-Neuve, Belgium
| | - Emile A Schweikert
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3144, USA
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13
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Tian H, Maciążek D, Postawa Z, Garrison BJ, Winograd N. CO2 Cluster Ion Beam, an Alternative Projectile for Secondary Ion Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1476-82. [PMID: 27324648 PMCID: PMC5199235 DOI: 10.1007/s13361-016-1423-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/14/2016] [Accepted: 05/19/2016] [Indexed: 05/18/2023]
Abstract
The emergence of argon-based gas cluster ion beams for SIMS experiments opens new possibilities for molecular depth profiling and 3D chemical imaging. These beams generally leave less surface chemical damage and yield mass spectra with reduced fragmentation compared with smaller cluster projectiles. For nanoscale bioimaging applications, however, limited sensitivity due to low ionization probability and technical challenges of beam focusing remain problematic. The use of gas cluster ion beams based upon systems other than argon offer an opportunity to resolve these difficulties. Here we report on the prospects of employing CO2 as a simple alternative to argon. Ionization efficiency, chemical damage, sputter rate, and beam focus are investigated on model compounds using a series of CO2 and Ar cluster projectiles (cluster size 1000-5000) with the same mass. The results show that the two projectiles are very similar in each of these aspects. Computer simulations comparing the impact of Ar2000 and (CO2)2000 on an organic target also confirm that the CO2 molecules in the cluster projectile remain intact, acting as a single particle of m/z 44. The imaging resolution employing CO2 cluster projectiles is improved by more than a factor of two. The advantage of CO2 versus Ar is also related to the increased stability which, in addition, facilitates the operation of the gas cluster ion beams (GCIB) system at lower backing pressure. Graphical Abstract ᅟ.
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Affiliation(s)
- Hua Tian
- Chemistry Department, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Dawid Maciążek
- Smoluchowski Institute of Physics, Jagiellonian University, ulica Lojasiewicza 11, 30-348, Krakow, Poland
| | - Zbigniew Postawa
- Smoluchowski Institute of Physics, Jagiellonian University, ulica Lojasiewicza 11, 30-348, Krakow, Poland
| | - Barbara J Garrison
- Chemistry Department, Pennsylvania State University, University Park, PA, 16802, USA
| | - Nicholas Winograd
- Chemistry Department, Pennsylvania State University, University Park, PA, 16802, USA
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14
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Rzeznik L, Fleming Y, Wirtz T, Philipp P. Experimental and simulation-based investigation of He, Ne and Ar irradiation of polymers for ion microscopy. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2016; 7:1113-28. [PMID: 27547629 PMCID: PMC4979758 DOI: 10.3762/bjnano.7.104] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/14/2016] [Indexed: 05/28/2023]
Abstract
Secondary ion mass spectrometry (SIMS) on the helium ion microscope (HIM) promises higher lateral resolution than on classical SIMS instruments. However, full advantage of this new technique can only be obtained when the interaction of He(+) or Ne(+) primary ions with the sample is fully controlled. In this work we investigate how He(+) and Ne(+) bombardment influences roughness formation and preferential sputtering for polymer samples and how they compare to Ar(+) primary ions used in classical SIMS by combining experimental techniques with Molecular Dynamics (MD) simulations and SD_TRIM_SP modelling. The results show that diffusion coefficients for He, Ne and Ar in polymers are sufficiently high to prevent any accumulation of rare gas atoms in the polymers which could lead to some swelling and bubble formation. Roughness formation was also not observed. Preferential sputtering is more of a problem, with enrichment of carbon up to surface concentrations above 80%. In general, the preferential sputtering is largely depending on the primary ion species and the impact energies. For He(+) bombardment, it is more of an issue for low keV impact energies and for the heavier primary ion species the preferential sputtering is sample dependent. For He(+) steady state conditions are reached for fluences much higher than 10(18) ions/cm(2). For Ne(+) and Ar(+), the transient regime extends up to fluences of 10(17)-10(18) ions/cm(2). Hence, preferential sputtering needs to be taken into account when interpreting images recorded under He(+) or Ne(+) bombardment on the HIM.
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Affiliation(s)
- Lukasz Rzeznik
- Advanced Instrumentation for Ion Nano-Analytics (AINA), MRT Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Yves Fleming
- Advanced Instrumentation for Ion Nano-Analytics (AINA), MRT Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Tom Wirtz
- Advanced Instrumentation for Ion Nano-Analytics (AINA), MRT Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Patrick Philipp
- Advanced Instrumentation for Ion Nano-Analytics (AINA), MRT Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, L-4422 Belvaux, Luxembourg
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15
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Verkhoturov SV, Geng S, Czerwinski B, Young AE, Delcorte A, Schweikert EA. Single impacts of keV fullerene ions on free standing graphene: Emission of ions and electrons from confined volume. J Chem Phys 2015; 143:164302. [DOI: 10.1063/1.4933310] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
| | - Sheng Geng
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3144, USA
| | - Bartlomiej Czerwinski
- Institute of Condensed Matter and Nanosciences–Bio and Soft Matter (IMCN/BSMA), Université Catholique de Louvain, 1 Croix du Sud, B-1348 Louvain-la-Neuve, Belgium
- Applied Physics, Division of Materials Science, Department of Engineering Sciences and Mathematics, Luleå University of Technology, SE-971 87 Luleå, Sweden
| | - Amanda E. Young
- Materials Characterization Facility, Texas A&M University, College Station, Texas 77843-3122, USA
| | - Arnaud Delcorte
- Institute of Condensed Matter and Nanosciences–Bio and Soft Matter (IMCN/BSMA), Université Catholique de Louvain, 1 Croix du Sud, B-1348 Louvain-la-Neuve, Belgium
| | - Emile A. Schweikert
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3144, USA
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16
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Philipp P, Angerer TB, Sämfors S, Blenkinsopp P, Fletcher JS, Wirtz T. Significant enhancement of negative secondary ion yields by cluster ion bombardment combined with cesium flooding. Anal Chem 2015; 87:10025-32. [PMID: 26378890 DOI: 10.1021/acs.analchem.5b02635] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In secondary ion mass spectrometry (SIMS), the beneficial effect of cesium implantation or flooding on the enhancement of negative secondary ion yields has been investigated in detail for various semiconductor and metal samples. All results have been obtained for monatomic ion bombardment. Recent progress in SIMS is based to a large extent on the development and use of cluster primary ions. In this work we show that the enhancement of negative secondary ions induced by the combination of ion bombardment with simultaneous cesium flooding is valid not only for monatomic ion bombardment but also for cluster primary ions. Experiments carried out using C60+ and Ar4000+ bombardment on silicon show that yields of negative secondary silicon ions can be optimized in the same way as by Ga+ and Cs+ bombardment. Both for monatomic and cluster ion bombardment, the optimization does not depend on the primary ion species. Hence, it can be assumed that the silicon results are also valid for other cluster primary ions and that results obtained for monatomic ion bombardment on other semiconductor and metal samples are also valid for cluster ion bombardment. In SIMS, cluster primary ions are also largely used for the analysis of organic matter. For polycarbonate, our results show that Ar4000+ bombardment combined with cesium flooding enhances secondary ion signals by a factor of 6. This can be attributed to the removal of charging effects and/or reduced fragmentation, but no major influence on ionization processes can be observed. The use of cesium flooding for the imaging of cells was also investigated and a significant enhancement of secondary ion yields was observed. Hence, cesium flooding has also a vast potential for SIMS analyses with cluster ion bombardment.
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Affiliation(s)
- Patrick Philipp
- Advanced Instrumentation for Ion Nano-Analytics (AINA), MRT Department, Luxembourg Institute of Science and Technology (LIST) , L-4422 Belvaux, Luxembourg
| | - Tina B Angerer
- Department of Chemistry and Molecular Biology, University of Gothenburg , SE-412 96, Gothenburg, Sweden
| | - Sanna Sämfors
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology , SE-412 90 Gothenburg, Sweden
| | | | - John S Fletcher
- Department of Chemistry and Molecular Biology, University of Gothenburg , SE-412 96, Gothenburg, Sweden.,Department of Chemistry and Chemical Engineering, Chalmers University of Technology , SE-412 90 Gothenburg, Sweden
| | - Tom Wirtz
- Advanced Instrumentation for Ion Nano-Analytics (AINA), MRT Department, Luxembourg Institute of Science and Technology (LIST) , L-4422 Belvaux, Luxembourg
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17
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Abstract
Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a rapidly developing technique for the characterization of a wide range of materials. Recently, advances in instrumentation and sample preparation approaches have provided the ability to perform 3D molecular imaging experiments. Polyatomic ion beams, such as C60, and gas cluster ion beams, often Arn (n = 500-4000), substantially reduce the subsurface damage accumulation associated with continued bombardment of organic samples with atomic beams. In this review, the capabilities of the technique are discussed and examples of the 3D imaging approach for the analysis of model membrane systems, plant single cell, and tissue samples are presented. Ongoing challenges for 3D ToF-SIMS imaging are also discussed along with recent developments that might offer improved 3D imaging prospects in the near future.
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18
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Bich C, Touboul D, Brunelle A. Cluster TOF-SIMS imaging as a tool for micrometric histology of lipids in tissue. MASS SPECTROMETRY REVIEWS 2014; 33:442-51. [PMID: 24265115 DOI: 10.1002/mas.21399] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Revised: 02/20/2013] [Accepted: 03/17/2013] [Indexed: 05/20/2023]
Abstract
Recent developments in instrumentation, ion beams or analyzers, for cluster time-of-flight secondary ion mass spectrometry (TOF-SIMS) imaging are described here. The methods which are employed to increase the sensitivity or to perform three-dimensional analyses in the organic materials are also illustrated. This review shows the improvements made for lipid imaging by cluster TOF-SIMS in various types of material and applications, and gives reasons for the expansion of its utilization.
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Affiliation(s)
- Claudia Bich
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles, CNRS, Avenue de la Terrasse, 91198, Gif-sur-Yvette Cedex, France
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19
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Krantzman KD, Briner CA, Garrison BJ. Investigation of carbon buildup in simulations of multi-impact bombardment of Si with 20 keV C60 projectiles. J Phys Chem A 2014; 118:8081-7. [PMID: 24527764 DOI: 10.1021/jp4108624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Beams of single C(+) ions are used for the incorporation of Si in the synthesis of thin films of SiC, which have a wide range of technological applications. We present a theoretical investigation of the use of C60 cluster beams to produce thin films of SiC on a Si substrate, which demonstrates that there are potential advantages to using C60(+) cluster ion beams over C(+) single ion beams. Molecular dynamics simulations of the multi-impact bombardment of Si with 20 keV normal incident C60 projectiles are performed to study the buildup of carbon and the formation of a region of Si-C mixing up to a fluence of 1.6 impacts/nm(2) (900 impacts). The active region of the Si solid is defined as the portion of target that contains almost all of the C atoms and the height ranges from 3 nm to more than 7 nm below the average surface height. The C fraction in the active region is calculated as a function of fluence, and a simple model is developed to describe the dependence of the C fraction on fluence. An analytic function from this model is fit to the data from the molecular dynamics simulations and extrapolated to predict the fluence necessary to achieve equilibrium conditions in which the C fraction is constant with fluence. The fraction of C atoms at equilibrium is predicted to be 0.19, and the fluence necessary to achieve 90% of this asymptotic maximum value is equal to 4.0 impacts/nm(2).
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Affiliation(s)
- Kristin D Krantzman
- Department of Chemistry and Biochemistry, College of Charleston , 66 George Street, Charleston, South Carolina 29424, United States
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20
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Paruch RJ, Garrison BJ, Mlynek M, Postawa Z. On Universality in Sputtering Yields Due to Cluster Bombardment. J Phys Chem Lett 2014; 5:3227-3230. [PMID: 26276337 DOI: 10.1021/jz501545t] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Molecular dynamics simulations, in which atomic and molecular solids are bombarded by Arn (n = 60-2953) clusters, are used to explain the physics that underlie the "universal relation" of the sputtering yield Y per cluster atom versus incident energy E per cluster atom (Y/n vs E/n). We show that a better representation to unify the results is Y/(E/U0) versus (E/U0)/n, where U0 is the sample cohesive energy per atom or molecular equivalent, and the yield Y is given in the units of atoms or molecular equivalents for atomistic and molecular solids, respectively. In addition, we identified a synergistic cluster effect. Specifically, for a given (E/U0)/n value, larger clusters produce larger yields than the yields that are only proportional to the cluster size n or equivalently to the scaled energy E/U0. This synergistic effect can be described in the high (E/U0)/n regime as scaling of Y with (E/U0)(α), where α > 1.
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Affiliation(s)
- Robert J Paruch
- †Department of Chemistry, 104 Chemistry Building, Penn State University, University Park, Pennsylvania 16802, United States
| | - Barbara J Garrison
- †Department of Chemistry, 104 Chemistry Building, Penn State University, University Park, Pennsylvania 16802, United States
| | - Maksymilian Mlynek
- ‡Smoluchowski Institute of Physics, Jagiellonian University, ulica Reymonta 4, 30-059 Krakow, Poland
| | - Zbigniew Postawa
- ‡Smoluchowski Institute of Physics, Jagiellonian University, ulica Reymonta 4, 30-059 Krakow, Poland
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21
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Czerwinski B, Delcorte A. Chemistry and sputtering induced by fullerene and argon clusters in carbon-based materials. SURF INTERFACE ANAL 2014. [DOI: 10.1002/sia.5637] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Bartlomiej Czerwinski
- Institute of Condensed Matter and Nanosciences - Bio & Soft Matter (IMCN/BSMA); Université catholique de Louvain; 1 Croix du Sud B-1348 Louvain-la-Neuve Belgium
| | - Arnaud Delcorte
- Institute of Condensed Matter and Nanosciences - Bio & Soft Matter (IMCN/BSMA); Université catholique de Louvain; 1 Croix du Sud B-1348 Louvain-la-Neuve Belgium
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22
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Carlred L, Gunnarsson A, Solé-Domènech S, Johansson B, Vukojević V, Terenius L, Codita A, Winblad B, Schalling M, Höök F, Sjövall P. Simultaneous Imaging of Amyloid-β and Lipids in Brain Tissue Using Antibody-Coupled Liposomes and Time-of-Flight Secondary Ion Mass Spectrometry. J Am Chem Soc 2014; 136:9973-81. [DOI: 10.1021/ja5019145] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Louise Carlred
- Chemistry,
Materials and Surfaces, SP Technical Research Institute of Sweden, P.O. Box 857, SE-501 15 Borås, Sweden
- Department
of Applied Physics, Division of Biological Physics, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
| | - Anders Gunnarsson
- Department
of Applied Physics, Division of Biological Physics, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
| | - Santiago Solé-Domènech
- Department
of Molecular Medicine and Surgery, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Björn Johansson
- Department
of Molecular Medicine and Surgery, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Vladana Vukojević
- Department
of Clinical Neuroscience, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Lars Terenius
- Department
of Clinical Neuroscience, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Alina Codita
- Department
of Neurobiology, Care Sciences and Society, KI Alzheimer Disease Research
Center, Karolinska Institutet, SE-141 86 Stockholm, Sweden
| | - Bengt Winblad
- Department
of Neurobiology, Care Sciences and Society, KI Alzheimer Disease Research
Center, Karolinska Institutet, SE-141 86 Stockholm, Sweden
| | - Martin Schalling
- Department
of Molecular Medicine and Surgery, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Fredrik Höök
- Department
of Applied Physics, Division of Biological Physics, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
| | - Peter Sjövall
- Chemistry,
Materials and Surfaces, SP Technical Research Institute of Sweden, P.O. Box 857, SE-501 15 Borås, Sweden
- Department
of Applied Physics, Division of Biological Physics, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
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23
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Delcorte A, Restrepo OA, Hamraoui K, Czerwinski B. Cluster impacts in organics: microscopic models and universal sputtering curves. SURF INTERFACE ANAL 2014. [DOI: 10.1002/sia.5544] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Arnaud Delcorte
- Institute of Condensed Matter and Nanosciences - Bio and Soft Matter (IMCN/BSMA); Université catholique de Louvain; 1 Croix du Sud B-1348 Louvain-la-Neuve Belgium
| | - Oscar A. Restrepo
- Institute of Condensed Matter and Nanosciences - Bio and Soft Matter (IMCN/BSMA); Université catholique de Louvain; 1 Croix du Sud B-1348 Louvain-la-Neuve Belgium
| | - Karim Hamraoui
- Institute of Condensed Matter and Nanosciences - Bio and Soft Matter (IMCN/BSMA); Université catholique de Louvain; 1 Croix du Sud B-1348 Louvain-la-Neuve Belgium
| | - Bartlomiej Czerwinski
- Institute of Condensed Matter and Nanosciences - Bio and Soft Matter (IMCN/BSMA); Université catholique de Louvain; 1 Croix du Sud B-1348 Louvain-la-Neuve Belgium
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24
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Postawa Z, Kanski M, Maciazek D, Paruch RJ, Garrison BJ. Computer simulations of sputtering and fragment formation during keV C60
bombardment of octane and β
-carotene. SURF INTERFACE ANAL 2014. [DOI: 10.1002/sia.5550] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Zbigniew Postawa
- Smoluchowski Institute of Physics; Jagiellonian University; ul. Reymonta 4 30-059 Krakow Poland
| | - Michal Kanski
- Smoluchowski Institute of Physics; Jagiellonian University; ul. Reymonta 4 30-059 Krakow Poland
| | - Dawid Maciazek
- Smoluchowski Institute of Physics; Jagiellonian University; ul. Reymonta 4 30-059 Krakow Poland
| | - Robert J. Paruch
- Department of Chemistry; Penn State University; 104 Chemistry Building, University Park PA 16802 USA
| | - Barbara J. Garrison
- Department of Chemistry; Penn State University; 104 Chemistry Building, University Park PA 16802 USA
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25
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Paruch RJ, Postawa Z, Garrison BJ. How material properties affect depth profiles - insight from computer modeling. SURF INTERFACE ANAL 2014. [DOI: 10.1002/sia.5423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Robert J. Paruch
- Department of Chemistry; Penn State University; 104 Chemistry Building University Park PA 16802 USA
| | - Zbigniew Postawa
- Smoluchowski Institute of Physics; Jagiellonian University; ul. Reymonta 4 30-059 Krakow Poland
| | - Barbara J. Garrison
- Department of Chemistry; Penn State University; 104 Chemistry Building University Park PA 16802 USA
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26
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Kraft ML, Klitzing HA. Imaging lipids with secondary ion mass spectrometry. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1841:1108-19. [PMID: 24657337 DOI: 10.1016/j.bbalip.2014.03.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 03/11/2014] [Accepted: 03/12/2014] [Indexed: 10/25/2022]
Abstract
This review discusses the application of time-of-flight secondary ion mass spectrometry (TOF-SIMS) and magnetic sector SIMS with high lateral resolution performed on a Cameca NanoSIMS 50(L) to imaging lipids. The similarities between the two SIMS approaches and the differences that impart them with complementary strengths are described, and various strategies for sample preparation and to optimize the quality of the SIMS data are presented. Recent reports that demonstrate the new insight into lipid biochemistry that can be acquired with SIMS are also highlighted. This article is part of a Special Issue entitled Tools to study lipid functions.
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Affiliation(s)
- Mary L Kraft
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Haley A Klitzing
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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27
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Weidner T, Castner DG. SFG analysis of surface bound proteins: a route towards structure determination. Phys Chem Chem Phys 2013; 15:12516-24. [PMID: 23727992 PMCID: PMC3732458 DOI: 10.1039/c3cp50880c] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The surface of a material is rapidly covered with proteins once that material is placed in a biological environment. The structure and function of these bound proteins play a key role in the interactions and communications of the material with the biological environment. Thus, it is crucial to gain a molecular level understanding of surface bound protein structure. While X-ray diffraction and solution phase NMR methods are well established for determining the structure of proteins in the crystalline or solution phase, there is not a corresponding single technique that can provide the same level of structural detail about proteins at surfaces or interfaces. However, recent advances in sum frequency generation (SFG) vibrational spectroscopy have significantly increased our ability to obtain structural information about surface bound proteins and peptides. A multi-technique approach of combining SFG with (1) protein engineering methods to selectively introduce mutations and isotopic labels, (2) other experimental methods such as time-of-flight secondary ion mass spectrometry (ToF-SIMS) and near edge X-ray absorption fine structure (NEXAFS) to provide complementary information, and (3) molecular dynamic (MD) simulations to extend the molecular level experimental results is a particularly promising route for structural characterization of surface bound proteins and peptides. By using model peptides and small proteins with well-defined structures, methods have been developed to determine the orientation of both backbone and side chains to the surface.
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Affiliation(s)
- Tobias Weidner
- National ESCA and Surface Analysis Center for Biomedical Problems (NESAC/BIO), Molecular Engineering and Sciences Institute, Department of Bioengineering, Box 351653, University of Washington, Seattle, WA 98195-1653
| | - David G. Castner
- National ESCA and Surface Analysis Center for Biomedical Problems (NESAC/BIO), Molecular Engineering and Sciences Institute, Department of Bioengineering, Box 351653, University of Washington, Seattle, WA 98195-1653
- National ESCA and Surface Analysis Center for Biomedical Problems (NESAC/BIO), Molecular Engineering and Sciences Institute, Department of Chemical Engineering, Box 351653, University of Washington, Seattle, WA 98195-1653
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28
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Gnaser H, Fujii M, Nakagawa S, Seki T, Aoki T, Matsuo J. Peptide dissociation patterns in secondary ion mass spectrometry under large argon cluster ion bombardment. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:1490-1496. [PMID: 23722683 DOI: 10.1002/rcm.6599] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 04/08/2013] [Accepted: 04/14/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE The analysis of organic and biological substances by secondary ion mass spectrometry (SIMS) has greatly benefited from the use of cluster ions as primary bombarding species. Thereby, depth profiling and three-dimensional (3D) imaging of such systems became feasible. Large Ar(n)(+) cluster ions may constitute a further improvement in this direction. METHODS To explore this option, large Ar(n)(+) cluster ions (with n ~1500 Ar atoms per cluster) were used to investigate the emission of positive secondary ions from two peptide specimens (angiotensin I and bradykinin) by orthogonal time-of-flight SIMS using bombarding energies 6, 10 and 14 keV. RESULTS For both peptides, the protonated molecular ion is observed in the mass spectra. In addition, distinct fragmentation patterns were observed; these indicate that fragment ions under Ar cluster irradiation form primarily via cleavage of bonds along the peptide backbone whereas the rapture of side chains occurs much less frequently. These features appear to be similar to low-energy collision-induced dissociation pathways. CONCLUSIONS Tentatively, these findings can then be ascribed to the concerted action of the large number of Ar atoms in the impact zone of cluster at the surface: these low-energy Ar species (with an average energy of few eV) may effect the cleavage of the peptide bonds and lead, eventually, to the emission of the fragment ions.
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Affiliation(s)
- Hubert Gnaser
- Department of Physics and Research Center OPTIMAS, University of Kaiserslautern, Kaiserslautern, Germany.
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29
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Restrepo OA, Gonze X, Bertrand P, Delcorte A. Computer simulations of cluster impacts: effects of the atomic masses of the projectile and target. Phys Chem Chem Phys 2013; 15:7621-7. [PMID: 23591660 DOI: 10.1039/c3cp50346a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cluster secondary ion mass spectrometry is now widely used for the characterization of nanostructures. In order to gain a better understanding of the physics of keV cluster bombardment of surfaces and nanoparticles (NPs), the effects of the atomic masses of the projectile and of the target on the energy deposition and induced sputtering have been studied by means of molecular dynamics simulations. 10 keV C60 was used as a model projectile and impacts on both a flat polymer surface and a metal NP were analyzed. In the first case, the mass of the impinging carbon atoms was artificially varied and, in the second case, the mass of the NP atoms was varied. The results can be rationalized on the basis of the different atomic mass ratios of the projectile and target. In general, the emission is at its maximum, when the projectile and target have the same atomic masses. In the case of the supported NP, the emission of the underlying organic material increases as the atomic mass of the NP decreases. However, it is always less than that calculated for the bare organic surface, irrespective of the mass ratio. The results obtained with C60 impacts on the flat polymer are also compared to simulations of C60 and monoatomic Ga impacts on the NP.
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Affiliation(s)
- Oscar A Restrepo
- Institute of Condensed Matter and Nanosciences, Université catholique de Louvain, Croix du Sud, 1 bte 3, B-1348 Louvain-la-Neuve, Belgium.
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30
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Lee BJ, Baur M, Gebhardt CR, Dürr M. Quantification of the ionization probability during desorption/ionization of oligopeptides induced by neutral cluster impact. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:1090-1094. [PMID: 23592213 DOI: 10.1002/rcm.6550] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 01/18/2013] [Accepted: 02/17/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE Desorption-and-ionization induced by neutral cluster impact is a soft and matrix-free method, which leads to the formation of free ions of oligopeptides and smaller proteins without fragmentation. As a prerequisite for its successful application in bioanalytics, especially with respect to sensitivity, the ionization efficiency, i.e., the ion-to-neutral ratio of the desorbing molecules, was determined. METHODS Neutral SO2 clusters of 10(3) to 10(4) molecules in size were seeded in a pulsed He beam and used to desorb and ionize oligopeptides by means of cluster surface impact. The samples were prepared by drop casting a well-defined amount of substance on the substrate surface; the desorbing ions were identified by means of time-of-flight mass spectrometry. Furthermore, the ion current leaving the surface was determined for positive ions, which predominate in the investigated oligopeptides. RESULTS For angiotensin II, bradykinin (1-7), and adrenocorticotropic hormone (34-39), the number of ions desorbed from the respective samples was compared with the amount of substance applied on the substrate. Assuming that all biomolecules were desorbed during the experiment, the ion-to-neutral ratio or ionization efficiency η was determined. For the tested molecules, values of η between 0.5% and 3% were observed; the substrate material and the total amount of substance applied were shown to have a minor effect on the results. CONCLUSIONS The ion-to-neutral ratio in desorption/ionization of oligopeptides induced by neutral cluster impact was determined to be of the order of 10(-3) to 10(-2). The soft and matrix-free nature of the method in combination with this value of η might be interesting for applications in bioanalytics.
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Affiliation(s)
- B-J Lee
- Fakultät Angewandte Naturwissenschaften, Hochschule Esslingen, Esslingen, Germany
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31
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Kennedy PE, Postawa Z, Garrison BJ. Dynamics Displayed by Energetic C60 Bombardment of Metal Overlayers on an Organic Substrate. Anal Chem 2013; 85:2348-55. [DOI: 10.1021/ac303348y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Paul E. Kennedy
- Department of Chemistry, 104
Chemistry Building, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Zbigniew Postawa
- Smoluchowski Institute of Physics, Jagiellonian University, ul. Reymonta 4, 30-059 Kraków,
Poland
| | - Barbara J. Garrison
- Department of Chemistry, 104
Chemistry Building, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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32
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Tejero R, Rossbach P, Keller B, Anitua E, Reviakine I. Time-of-flight secondary ion mass spectrometry with principal component analysis of titania-blood plasma interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:902-912. [PMID: 23095019 DOI: 10.1021/la303360f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Treatment of osseoimplant surfaces with autologous platelet-rich plasma prepared according to the plasma rich in growth factors (PRGF-Endoret) protocol prior to implantation yields promising results in the clinic. Our objective is to understand the organization of complex interfaces between blood plasma preparations of various compositions and model titania surfaces. Here we present the results of the morphological and chemical characterization of TiO(2) surfaces incubated with four types of blood plasma preparations devoid of leukocytes and red blood cells: either enriched in platelets (PRGF-Endoret) or platelet-depleted, and either activated with CaCl(2) to induce clotting, or not. Chemical characterization was done by time-of-flight secondary ion mass spectrometry with principal component analysis (ToF-SIMS/PCA). The interface morphology was studied with scanning electron and atomic force microscopy. Immunofluorescence microscopy was used to identify platelets and infer their activation state. We observe clear differences among the four types of interfaces by ToF-SIMS/PCA. Some of these could be straightforwardly related to the differences in the sample morphology and known effects of platelet activation, but others are more subtle. Strikingly, it was possible to differentiate between these samples by ToF-SIMS/PCA of the protein species alone. This clearly indicates that the composition, orientation, and/or conformation of the proteins in these specimens depend both on the platelets' presence and on their activation. The ToF-SIMS imaging functionality furthermore provides unique insight into the distribution of phospholipid species in these samples.
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33
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Brenes DA, Postawa Z, Wucher A, Blenkinsopp P, Garrison BJ, Winograd N. An experimental and theoretical view of energetic C 60 cluster bombardment onto molecular solids. SURF INTERFACE ANAL 2013; 45:50-53. [PMID: 26311917 PMCID: PMC4547361 DOI: 10.1002/sia.5077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recent experimental measurements and calculations performed by molecular dynamics computer simulations indicate, for highly energetic C60 primary ions bombarding molecular solids, the emission of intact molecules is unique. An energy- and angle-resolved neutral mass spectrometer coupled with laser photoionization techniques was used to measure the polar angle distribution of neutral benzo[a]pyrene molecules desorbed by 20-keV [Formula: see text] primary ions and observed to peak at off-normal angles integrated over all possible emission energies. Similarly, computer simulations of 20-keV C60 projectiles bombarding a coarse-grained benzene system resulted in calculations of nearly identical polar angle distributions. Upon resolving the measured and calculated polar angle distributions, sputtered molecules with high kinetic energies are the primary contributors to the off-normal peak. Molecules with low kinetic energies were measured and calculated to desorb broadly peaked about the surface normal. The computer simulations suggest the fast deposition of energy from the C60 impact promotes the molecular emission by fluid-flow and effusive-type motions. The signature of off-normal emission angles is unique for molecules because fragmentation processes remove molecules that would otherwise eject near normal to the surface. Experimental measurements from a Ni {001} single crystal bombarded by 20-keV [Formula: see text] demonstrate the absence of this unique signature.
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Affiliation(s)
- Daniel A. Brenes
- The Pennsylvania State University, Department of Chemistry, University Park, PA, 16802, USA
| | - Zbigniew Postawa
- Smoluchowski Institute of Physics, Jagiellonian Univeristy, ul. Reymonta 4, 30-059 Krakow, Poland
| | - Andreas Wucher
- Faculty of Physics, University of Duisburg-Essen, 47048 Duisburg, Germany
| | - Paul Blenkinsopp
- Ionoptika Ltd., Epsilon House Chilworth Science Park, Southampton SO53 4NF, U.K
| | - Barbara J. Garrison
- The Pennsylvania State University, Department of Chemistry, University Park, PA, 16802, USA
| | - Nicholas Winograd
- The Pennsylvania State University, Department of Chemistry, University Park, PA, 16802, USA
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34
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Fletcher JS, Vickerman JC. Secondary Ion Mass Spectrometry: Characterizing Complex Samples in Two and Three Dimensions. Anal Chem 2012; 85:610-39. [DOI: 10.1021/ac303088m] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- John S. Fletcher
- Manchester Institute
of Biotechnology, University of Manchester, Manchester M13 9PL, U.K
| | - John C. Vickerman
- Manchester Institute
of Biotechnology, University of Manchester, Manchester M13 9PL, U.K
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35
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Cyriac J, Pradeep T, Kang H, Souda R, Cooks RG. Low-Energy Ionic Collisions at Molecular Solids. Chem Rev 2012; 112:5356-411. [DOI: 10.1021/cr200384k] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Jobin Cyriac
- DST Unit of
Nanoscience, Department
of Chemistry, Indian Institute of Technology Madras, Chennai 600 036, India
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United
States
| | - T. Pradeep
- DST Unit of
Nanoscience, Department
of Chemistry, Indian Institute of Technology Madras, Chennai 600 036, India
| | - H. Kang
- Department of Chemistry, Seoul National University, Gwanak-gu, Seoul 151-747,
Republic of Korea
| | - R. Souda
- International
Center for Materials
Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - R. G. Cooks
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United
States
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36
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Kennedy PE, Garrison BJ. Chemical damage resulting from 15 keV C60
, Ar18
and Ar60
cluster bombardments of solid benzene. SURF INTERFACE ANAL 2012. [DOI: 10.1002/sia.5022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Paul E. Kennedy
- Department of Chemistry; The Pennsylvania State University; 104 Chemistry Building, University Park PA 16802 USA
| | - Barbara J. Garrison
- Department of Chemistry; The Pennsylvania State University; 104 Chemistry Building, University Park PA 16802 USA
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37
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Rzeznik L, Paruch R, Garrison BJ, Postawa Z. Sputtering of a coarse-grained benzene and Ag(111) crystals by large Ar clusters - effect of impact angle and cohesive energy. SURF INTERFACE ANAL 2012. [DOI: 10.1002/sia.4934] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Lukasz Rzeznik
- University of Information Technology and Management; Sucharskiego 2; Rzeszow; Poland
| | - Robert Paruch
- Institute of Physics; Jagiellonian University; Reymonta 4; Kraków; Poland
| | - Barbara J. Garrison
- Department of Chemistry; The Pennsylvania State University; University Park; PA; 16802; USA
| | - Zbigniew Postawa
- Institute of Physics; Jagiellonian University; Reymonta 4; Kraków; Poland
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38
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Cook EL, Krantzman KD, Garrison BJ. Surface topography effects in C60bombardment of Si. SURF INTERFACE ANAL 2012. [DOI: 10.1002/sia.4965] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Edward L. Cook
- Department of Chemistry and Biochemistry; 66 George Street, College of Charleston; Charleston; SC 29412; USA
| | - Kristin D. Krantzman
- Department of Chemistry and Biochemistry; 66 George Street, College of Charleston; Charleston; SC 29412; USA
| | - Barbara J. Garrison
- Department of Chemistry, 104 Chemistry Building; Penn State University, University Park; PA 16802; USA
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39
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Philipp P, Wirtz T, Kieffer J. Sputtering of silicon by low-energy oxygen bombardment studied by MD simulations. SURF INTERFACE ANAL 2012. [DOI: 10.1002/sia.4936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Patrick Philipp
- Department ‘Science and Analysis of Materials’ (SAM); Centre de Recherche Public - Gabriel Lippmann; 41 rue du Brill L-4422 Belvaux Luxembourg
| | - Tom Wirtz
- Department ‘Science and Analysis of Materials’ (SAM); Centre de Recherche Public - Gabriel Lippmann; 41 rue du Brill L-4422 Belvaux Luxembourg
| | - John Kieffer
- Department of Materials Science and Engineering; University of Michigan; Ann Arbor Michigan 48109-2136 USA
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40
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Delcorte A, Restrepo OA, Czerwinski B, Garrison BJ. Surface sputtering with nanoclusters: the relevant parameters. SURF INTERFACE ANAL 2012. [DOI: 10.1002/sia.4926] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- A. Delcorte
- Institute of Condensed Matter and Nanosciences; Université catholique de Louvain; 1 Croix du Sud B-1348 Louvain-la-Neuve Belgium
| | - O. A. Restrepo
- Institute of Condensed Matter and Nanosciences; Université catholique de Louvain; 1 Croix du Sud B-1348 Louvain-la-Neuve Belgium
| | - B. Czerwinski
- Institute of Condensed Matter and Nanosciences; Université catholique de Louvain; 1 Croix du Sud B-1348 Louvain-la-Neuve Belgium
| | - B. J. Garrison
- Department of Chemistry; The Pennsylvania State University; USA
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41
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Garrison BJ, Schiffer ZJ, Kennedy PE, Postawa Z. Modeling dynamic cluster SIMS experiments. SURF INTERFACE ANAL 2012. [DOI: 10.1002/sia.4905] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Barbara J. Garrison
- Department of Chemistry; Penn State University; University Park PA 16802 USA
| | - Zachary J. Schiffer
- Department of Chemistry; Penn State University; University Park PA 16802 USA
| | - Paul E. Kennedy
- Department of Chemistry; Penn State University; University Park PA 16802 USA
| | - Zbigniew Postawa
- Smoluchowski Institute of Physics; Jagiellonian University; ul. Reymonta 4 30-059 Kraków Poland
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42
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Postawa Z, Paruch R, Rzeznik L, Garrison BJ. Dynamics of large Ar cluster bombardment of organic solids. SURF INTERFACE ANAL 2012. [DOI: 10.1002/sia.4927] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Z. Postawa
- Smoluchowski Institute of Physics; Jagiellonian University; ul. Reymonta 4 30-059 Kraków Poland
| | - R. Paruch
- Smoluchowski Institute of Physics; Jagiellonian University; ul. Reymonta 4 30-059 Kraków Poland
| | - L. Rzeznik
- University of Information Technology and Management; ul. Sucharskiego 2 35-225 Rzeszow Poland
| | - B. J. Garrison
- Department of Chemistry; The Pennsylvania State University; University Park PA 16802 USA
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43
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44
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Fletcher JS, Rabbani S, Barber AM, Lockyer NP, Vickerman JC. Comparison of C60and GCIB primary ion beams for the analysis of cancer cells and tumour sections. SURF INTERFACE ANAL 2012. [DOI: 10.1002/sia.4874] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- John S. Fletcher
- Manchester Interdisciplinary Biocentre, School of Chemical Engineering and Analytical Science; University of Manchester; Manchester; M13 9PL; UK
| | - Sadia Rabbani
- Manchester Interdisciplinary Biocentre, School of Chemical Engineering and Analytical Science; University of Manchester; Manchester; M13 9PL; UK
| | | | - Nicholas P. Lockyer
- Manchester Interdisciplinary Biocentre, School of Chemical Engineering and Analytical Science; University of Manchester; Manchester; M13 9PL; UK
| | - John C. Vickerman
- Manchester Interdisciplinary Biocentre, School of Chemical Engineering and Analytical Science; University of Manchester; Manchester; M13 9PL; UK
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45
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Muramoto S, Brison J, Castner DG. Exploring the surface sensitivity of TOF-secondary ion mass spectrometry by measuring the implantation and sampling depths of Bi(n) and C60 ions in organic films. Anal Chem 2012; 84:365-72. [PMID: 22084828 PMCID: PMC3259203 DOI: 10.1021/ac202713k] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The surface sensitivity of Bi(n)(q+) (n = 1, 3, 5, q = 1, 2) and C(60)(q+) (q = 1, 2) primary ions in static time-of-flight secondary ion mass spectrometry (TOF-SIMS) experiments were investigated for molecular trehalose and polymeric tetraglyme organic films. Parameters related to surface sensitivity (impact crater depth, implantation depth, and molecular escape depths) were measured. Under static TOF-SIMS conditions (primary ion doses of 1 × 10(12) ions/cm(2)), the 25 keV Bi(1)(+) primary ions were the most surface sensitive with a molecular escape depth of 1.8 nm for protein films with tetraglyme overlayers, but they had the deepest implantation depth (~18 and 26 nm in trehalose and tetraglyme films, respectively). The 20 keV C(60)(+2) primary ions were the second most surface sensitive with a slightly larger molecular escape depth of 2.3 nm. The most important factor that determined the surface sensitivity of the primary ion was its impact crater depth or the amount of surface erosion. The most surface sensitive primary ions, Bi(1)(+) and C(60)(+2), created impact craters with depths of 0.3 and 1.0 nm, respectively, in tetraglyme films. In contrast, Bi(5)(+2) primary ions created impact craters with a depth of 1.8 nm in tetraglyme films and were the least surface sensitive with a molecular escape depth of 4.7 nm.
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Affiliation(s)
- Shin Muramoto
- National ESCA and Surface Analysis Center for Biomedical Problems, University of Washington, Seattle, WA 98195
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195
| | - Jeremy Brison
- National ESCA and Surface Analysis Center for Biomedical Problems, University of Washington, Seattle, WA 98195
- Department of Bioengineering, University of Washington, Seattle, WA 98195
| | - David G. Castner
- National ESCA and Surface Analysis Center for Biomedical Problems, University of Washington, Seattle, WA 98195
- Department of Bioengineering, University of Washington, Seattle, WA 98195
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195
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46
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Muramoto S, Graham DJ, Wagner MS, Lee TG, Moon DW, Castner DG. ToF-SIMS Analysis of Adsorbed Proteins: Principal Component Analysis of the Primary Ion Species Effect on the Protein Fragmentation Patterns. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2011; 115:24247-24255. [PMID: 22308191 PMCID: PMC3269828 DOI: 10.1021/jp208035x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In time-of-flight secondary ion mass spectrometry (ToF-SIMS), the choice of primary ion used for analysis can influence the resulting mass spectrum. This is because different primary ion types can produce different fragmentation pathways. In this study, analysis of single-component protein monolayers were performed using monatomic, tri-atomic, and polyatomic primary ion sources. Eight primary ions (Cs(+), Au(+), Au(3) (+), Bi(+), Bi(3) (+), Bi(3) (++), C(60) (+)) were used to examine to the low mass (m/z < 200) fragmentation patterns from five different proteins (bovine serum albumin, bovine serum fibrinogen, bovine immunoglobulin G and chicken egg white lysozyme) adsorbed onto mica surfaces. Principal component analysis (PCA) processing of the ToF-SIMS data showed that variation in peak intensity caused by the primary ions was greater than differences in protein composition. The spectra generated by Cs(+), Au(+) and Bi(+) primary ions were similar, but the spectra generated by monatomic, tri-atomic and polyatomic primary ion ions varied significantly. C(60) primary ions increased fragmentation of the adsorbed proteins in the m/z < 200 region, resulting in more intense low m/z peaks. Thus, comparison of data obtained by one primary ion species with that obtained by another primary ion species should be done with caution. However, for the spectra generated using a given primary ion beam, discrimination between the spectra of different proteins followed similar trends. Therefore, a PCA model of proteins created with a given ion source should only be applied to datasets obtained using the same ion source. The type of information obtained from PCA depended on the peak set used. When only amino acid peaks were used, PCA was able to identify the relationship between proteins by their amino acid composition. When all peaks from m/z 12-200 were used, PCA separated proteins based on a ratio of C(4)H(8)N(+) to K(+) peak intensities. This ratio correlated with the thickness of the protein films and Bi(1) (+) primary ions produced the most surface sensitive spectra.
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Affiliation(s)
- Shin Muramoto
- National ESCA and Surface Analysis Center for Biomedical Problems, University of Washington, Seattle, WA 98195
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195
| | - Daniel J. Graham
- National ESCA and Surface Analysis Center for Biomedical Problems, University of Washington, Seattle, WA 98195
- Department of Bioengineering, University of Washington, Seattle, WA 98195
| | | | - Tae Geol Lee
- Center for Nano-Bio Convergence, Korean Research Institute of Standards and Science, Daejeon 305-340, Korea
| | - Dae Won Moon
- Center for Nano-Bio Convergence, Korean Research Institute of Standards and Science, Daejeon 305-340, Korea
| | - David G. Castner
- National ESCA and Surface Analysis Center for Biomedical Problems, University of Washington, Seattle, WA 98195
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195
- Corresponding Author: Dept of Chemical Engineering Box 351750 University of Washington Seattle, WA 98195-1750 1-206-543-8094
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47
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Kostko O, Takahashi LK, Ahmed M. Desorption dynamics, internal energies, and imaging of organic molecules from surfaces with laser desorption and vacuum ultraviolet (VUV) photoionization. Chem Asian J 2011; 6:3066-76. [PMID: 21976383 DOI: 10.1002/asia.201100419] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Indexed: 11/11/2022]
Abstract
There is enormous interest in visualizing the chemical composition of organic material that comprises our world. A convenient method to obtain molecular information with high spatial resolution is imaging mass spectrometry. However, the internal energy deposited within molecules upon transfer to the gas phase from a surface can lead to increased fragmentation and to complications in analysis of mass spectra. Here it is shown that in laser desorption with postionization by tunable vacuum ultraviolet (VUV) radiation, the internal energy gained during laser desorption leads to minimal fragmentation of DNA bases. The internal temperature of laser-desorbed triacontane molecules approaches 670 K, whereas the internal temperature of thymine is 800 K. A synchrotron-based VUV postionization technique for determining translational temperatures reveals that biomolecules have translational temperatures in the range of 216-346 K. The observed low translational temperatures as well as their decrease with increased desorption laser power is explained by collisional cooling. An example of imaging mass spectrometry on an organic polymer by using laser-desorption VUV postionization shows 5 μm feature details while using a 30 μm laser spot size and 7 ns pulse duration. Applications of laser-desorption postionization to the analysis of cellulose, lignin, and humic acids are briefly discussed.
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Affiliation(s)
- Oleg Kostko
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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48
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Brenes DA, Postawa Z, Wucher A, Blenkinsopp P, Garrison BJ, Winograd N. Fluid Flow and Effusive Desorption: Dominant Mechanisms of Energy Dissipation after Energetic Cluster Bombardment of Molecular Solids. J Phys Chem Lett 2011; 2:2009-2014. [PMID: 21860689 PMCID: PMC3158660 DOI: 10.1021/jz200708j] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The angular distribution of intact organic molecules desorbed by energetic C(60) primary ions was probed both experimentally and with molecular dynamics computer simulations. For benzo[a]pyrene, the angular distribution of intact molecules is observed to peak at off-normal angles. Molecular dynamics computer simulations on a similar system show the mechanism of desorption involves fast deposition of energy followed by fluid-flow and effusive-type emission of intact molecules. The off-normal peak in the angular distribution is shown to arise from emission of intact molecules from the rim of a crater formed during the cluster impact. This signature is unique for molecules because fragmentation processes remove molecules that would otherwise eject at directions near-normal to the surface.
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Affiliation(s)
- Daniel A. Brenes
- The Pennsylvania State University, Department of Chemistry, University Park, PA 16802, USAdab390@psu
| | - Zbigniew Postawa
- Smoluchowski Institute of Physics, Jagiellonian University, ul. Reymonta 4, 30-059 Krakow, Poland
| | - Andreas Wucher
- Faculty of Physics, University of Duisburg-Essen, 47048 Duisburg, Germany
| | - Paul Blenkinsopp
- Ionoptika Ltd., Epsilon House, Chilworth Science Park, Southampton SO53 4NF, U.K.
| | - Barbara J. Garrison
- The Pennsylvania State University, Department of Chemistry, University Park, PA 16802, USA
| | - Nicholas Winograd
- The Pennsylvania State University, Department of Chemistry, University Park, PA 16802, USA
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49
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Baio JE, Weidner T, Interlandi G, Mendoza-Barrera C, Canavan HE, Michel R, Castner DG. Probing Albumin Adsorption onto Calcium Phosphates by XPS and ToF-SIMS. JOURNAL OF VACUUM SCIENCE AND TECHNOLOGY. B, NANOTECHNOLOGY & MICROELECTRONICS : MATERIALS, PROCESSING, MEASUREMENT, & PHENOMENA : JVST B 2011; 29:4D113. [PMID: 22267900 PMCID: PMC3260791 DOI: 10.1116/1.3613919] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 06/24/2011] [Indexed: 05/28/2023]
Abstract
In this study the binding and assembly of bovine serum albumin (BSA) onto three different calcium phosphate phases (hydroxyapatite, dibasic calcium phosphate dihydrate, and β-tricalcium phosphate) was investigated using a combination of X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). XPS was used to record adsorption isotherms and to quantify the amount of BSA adsorbed onto the different CaP surfaces. On all three surfaces a monolayer of adsorbed BSA was formed. ToF-SIMS was then used to investigate how the structure of BSA changes upon surface binding. ToF-SIMS data from BSA films on the three CaP surfaces showed intensity differences of secondary ions originating from both hydrophobic and hydrophilic amino acids. For a more quantitative examination of structural changes, we developed a ratio comparing the sum of intensities of secondary ions from hydrophobic and hydrophilic residues. A small, but statistically significant, increase in the value of this ratio (7%) was observed between a BSA film on hydroxyapatite versus dibasic calcium phosphate dihydrate. From this ratio we can make some initial hypotheses about what specific changes in BSA structure relate to these differences observed in the ToF-SIMS data.
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Affiliation(s)
- J E Baio
- National ESCA and Surface Analysis Center for Biomedical Problems, Department of Chemical, University of Washington, Seattle, WA 98195
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50
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Fletcher JS, Vickerman JC, Winograd N. Label free biochemical 2D and 3D imaging using secondary ion mass spectrometry. Curr Opin Chem Biol 2011; 15:733-40. [PMID: 21664172 DOI: 10.1016/j.cbpa.2011.05.016] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 05/19/2011] [Accepted: 05/20/2011] [Indexed: 11/24/2022]
Abstract
Time-of-flight secondary ion mass spectrometry (ToF-SIMS) provides a method for the detection of native and exogenous compounds in biological samples on a cellular scale. Through the development of novel ion beams the amount of molecular signal available from the sample surface has been increased. Through the introduction of polyatomic ion beams, particularly C(60), ToF-SIMS can now be used to monitor molecular signals as a function of depth as the sample is eroded thus proving the ability to generate 3D molecular images. Here we describe how this new capability has led to the development of novel instrumentation for 3D molecular imaging while also highlighting the importance of sample preparation and discuss the challenges that still need to be overcome to maximise the impact of the technique.
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Affiliation(s)
- John S Fletcher
- School of Chemical Engineering and Analytical Science, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester M1 7DN, UK.
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