Publications by authors named "Zbigniew Postawa"

23 Publications

  • Page 1 of 1

Three-Dimensional Mass Spectrometric Imaging of Biological Structures Using a Vacuum-Compatible Microfluidic Device.

Anal Chem 2020 10 16;92(20):13785-13793. Epub 2020 Sep 16.

Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.

Three-dimensional (3D) molecular imaging of biological structures is important for a wide range of research. In recent decades, secondary-ion mass spectrometry (SIMS) has been recognized as a powerful technique for both two-dimensional and 3D molecular imaging. Sample fixations (e.g., chemical fixation and cryogenic fixation methods) are necessary to adapt biological samples to the vacuum condition in the SIMS chamber, which has been demonstrated to be nontrivial and less controllable, thus limiting the wider application of SIMS on 3D molecular analysis of biological samples. Our group recently developed liquid SIMS that offers great opportunities for the molecular study of various liquids and liquid interfaces. In this work, we demonstrate that a further development of the vacuum-compatible microfluidic device used in liquid SIMS provides a convenient freeze-fixation of biological samples and leads to more controllable and convenient 3D molecular imaging. The special design of this new vacuum-compatible liquid chamber allows an easy determination of sputter rates of ice, which is critical for calibrating the depth scale of frozen biological samples. Sputter yield of a 20 keV Ar ion on ice has been determined as 1500 (±8%) water molecules per Ar ion, consistent with our results from molecular dynamics simulations. Moreover, using the information of ice sputter yield, we successfully conduct 3D molecular imaging of frozen homogenized milk and observe network structures of interesting organic and inorganic species. Taken together, our results will significantly benefit various research fields relying on 3D molecular imaging of biological structures.
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http://dx.doi.org/10.1021/acs.analchem.0c02204DOI Listing
October 2020

Intuitive Model of Surface Modification Induced by Cluster Ion Beams.

Anal Chem 2020 May 1;92(10):7349-7353. Epub 2020 May 1.

Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland.

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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http://dx.doi.org/10.1021/acs.analchem.0c01219DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7588020PMC
May 2020

Effect of the Impact Angle on the Kinetic Energy and Angular Distributions of β-Carotene Sputtered by 15 keV Ar Projectiles.

Anal Chem 2019 07 13;91(14):9161-9167. Epub 2019 Jun 13.

Smoluchowski Institute of Physics , Jagiellonian University , S. Lojasiewicza 11 , Kraków , Poland.

Molecular dynamics (MD) computer simulations are used to model ejection of particles from β-carotene samples bombarded by 15 keV Ar. The effect of the incidence angle on the angular and kinetic energy distributions is investigated. It has been found that both of these distributions are sensitive to the variation of the incidence angle, particularly near the normal incidence. For impacts along the surface normal, material ejection is azimuthally symmetric, and a significant emission occurs along the surface normal. The kinetic energy distribution of intact molecules has a maximum near 1 eV and terminates below approximately 2 eV. An increase of the incidence angle breaks the azimuthal symmetry. Most of the intact molecules become ejected in the forward direction. The maximum in the polar angle distribution shifts toward large off-normal angles. In addition, the most probable kinetic energy of ejected molecules is significantly increased. The mechanisms of molecular emission responsible for the observed changes are delineated. The implications of the observed ejection characteristics for the utilization of large gas cluster projectiles in secondary neutral mass spectrometry are discussed.
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http://dx.doi.org/10.1021/acs.analchem.9b01836DOI Listing
July 2019

Hypervelocity cluster ion impacts on free standing graphene: Experiment, theory, and applications.

J Chem Phys 2019 Apr;150(16):160901

Department of Chemistry, Texas A&M University, College Station, Texas 77843-3144, USA.

We present results from experiments and molecular dynamics (MD) simulations obtained with C and Au impacting on free-standing graphene, graphene oxide (GO), and graphene-supported molecular layers. The experiments were run on custom-built ToF reflectron mass spectrometers with C and Au-LMIS sources with acceleration potentials generating 50 keV C and 440-540 keV Au. Bombardment-detection was in the same mode as MD simulation, i.e., a sequence of individual projectile impacts with separate collection/identification of the ejecta from each impact in either the forward (transmission) or backward (reflection) direction. For C impacts on single layer graphene, the secondary ion (SI) yields for C and C emitted in transmission are ∼0.1 (10%). Similar yields were observed for analyte-specific ions from submonolayer deposits of phenylalanine. MD simulations show that graphene acts as a trampoline, i.e., they can be ejected without destruction. Another topic investigated dealt with the chemical composition of free-standing GO. The elemental composition was found to be approximately COH. We have also studied the impact of Au clusters on graphene. Again SI yields were high (e.g., 1.25 C/impact). 90-100 Au atoms evaporate off the exiting projectile which experiences an energy loss of ∼72 keV. The latter is a summation of energy spent on rupturing the graphene, ejecting carbon atoms and clusters and a dipole projectile/hole interaction. The charge distribution of the exiting projectiles is ∼50% neutrals and ∼25% either negatively or positively charged. We infer that free-standing graphene enables detection of attomole to zeptomole deposits of analyte via cluster-SI mass spectrometry.
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http://dx.doi.org/10.1063/1.5080606DOI Listing
April 2019

C-O Bond Dissociation and Induced Chemical Ionization Using High Energy (CO) Gas Cluster Ion Beam.

J Am Soc Mass Spectrom 2019 Mar 14;30(3):476-481. Epub 2018 Nov 14.

Chemistry Department, The Pennsylvania State University, 215 Chemistry Building, University Park, PA, 16802, USA.

A gas cluster ion beam (GCIB) source, consisting of CO 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 CO 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 CO clusters as they impact a surface under a variety of conditions. Clusters of (CO) (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 CO can be an effective cluster ion source for SIMS experiments. Graphical Abstract.
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http://dx.doi.org/10.1007/s13361-018-2102-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417932PMC
March 2019

"Trampoline" ejection of organic molecules from graphene and graphite via keV cluster ions impacts.

J Chem Phys 2018 Apr;148(14):144309

Department of Chemistry, Texas A&M University, College Station, Texas 77843-3144, USA.

We present the data on ejection of molecules and emission of molecular ions caused by single impacts of 50 keV C on a molecular layer of deuterated phenylalanine (D8Phe) deposited on free standing, 2-layer graphene. The projectile impacts on the graphene side stimulate the abundant ejection of intact molecules and the emission of molecular ions in the transmission direction. To gain insight into the mechanism of ejection, Molecular Dynamic simulations were performed. It was found that the projectile penetrates the thin layer of graphene, partially depositing the projectile's kinetic energy, and molecules are ejected from the hot area around the hole that is made by the projectile. The yield, Y, of negative ions of deprotonated phenylalanine, (D8Phe-H), emitted in the transmission direction is 0.1 ions per projectile impact. To characterize the ejection and ionization of molecules, we have performed the experiments on emission of (D8Phe-H) from the surface of bulk D8Phe (Y = 0.13) and from the single molecular layer of D8Phe deposited on bulk pyrolytic graphite (Y = 0.15). We show that, despite the similar yields of molecular ions, 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. The projectile impact on the graphene-D8Phe sample stimulates the collective radial movement of analyte atoms, which compresses the D8Phe layer radially from the hole. At the same time, this compression bends and stretches the graphene membrane around the hole thus accumulating potential energy. The accumulated potential energy is transformed into the kinetic energy of correlated movement upward for membrane atoms, thus the membrane acts as a trampoline for the molecules. The ejected molecules are effectively ionized; the ionization probability is ∼30× higher compared to that obtained for the bulk D8Phe target. The proposed mechanism of ionization involves tunneling of electrons from the vibrationally excited area around the hole to the molecules. Another proposed mechanism is a direct proton transfer exchange, which is suitable for a bulk target: ions of molecular fragments (i.e., CN) generated in the impact area interact with intact molecules from the rim of this area. There is a direct proton exchange process for the system D8Phe molecule + CN.
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http://dx.doi.org/10.1063/1.5021352DOI Listing
April 2018

Development of a Charge-Implicit ReaxFF Potential for Hydrocarbon Systems.

J Phys Chem Lett 2018 Jan 8;9(2):359-363. Epub 2018 Jan 8.

Department of Chemistry, Penn State University , 104 Chemistry Building, University Park, Pennsylvania 16802, United States.

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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http://dx.doi.org/10.1021/acs.jpclett.7b03155DOI Listing
January 2018

CO2 Cluster Ion Beam, an Alternative Projectile for Secondary Ion Mass Spectrometry.

J Am Soc Mass Spectrom 2016 09 20;27(9):1476-82. Epub 2016 Jun 20.

Chemistry Department, Pennsylvania State University, University Park, PA, 16802, USA.

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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http://dx.doi.org/10.1007/s13361-016-1423-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5199235PMC
September 2016

Effect of Oxygen Chemistry in Sputtering of Polymers.

J Phys Chem Lett 2016 Apr 12;7(8):1559-62. Epub 2016 Apr 12.

Smoluchowski Institute of Physics, Jagiellonian University , ul. Lojasiewicza 11, 30-348 Krakow, Poland.

Molecular dynamics computer simulations are used to model kiloelectronvolt cluster bombardment of pure hydrocarbon [polyethylene (PE) and polystyrene (PS)] and oxygen-containing [paraformaldehyde (PFA) and polylactic acid (PLA)] polymers by 20 keV C60 projectiles at a 45° impact angle to investigate the chemical effect of oxygen in the substrate material on the sputtering process. The simulations demonstrate that the presence of oxygen enhances the formation of small molecules such as carbon monoxide, carbon dioxide, water, and various molecules containing C═O double bonds. The explanation for the enhanced small molecule formation is the stability of carbon and oxygen multiple bonds relative to multiple bonds with only carbon atoms. This chemistry is reflected in the fraction of the ejected material that has a mass not higher than 104 amu. For PFA and PLA, the fraction is approximately 90% of the total mass, whereas for PE and PS, it is less than half.
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http://dx.doi.org/10.1021/acs.jpclett.6b00514DOI Listing
April 2016

On Universality in Sputtering Yields Due to Cluster Bombardment.

J Phys Chem Lett 2014 Sep 8;5(18):3227-30. Epub 2014 Sep 8.

‡Smoluchowski Institute of Physics, Jagiellonian University, ulica Reymonta 4, 30-059 Krakow, Poland.

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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http://dx.doi.org/10.1021/jz501545tDOI Listing
September 2014

Seduction of Finding Universality in Sputtering Yields Due to Cluster Bombardment of Solids.

Acc Chem Res 2015 Sep 7;48(9):2529-36. Epub 2015 Aug 7.

Department of Chemistry, Penn State University , 104 Chemistry Building, University Park, Pennsylvania 16802, United States.

Universal descriptions are appealing because they simplify the description of different (but similar) physical systems, allow the determination of general properties, and have practical applications. Recently, the concept of universality has been applied to the dependence of the sputtering (ejection) yield due to energetic cluster bombardment versus the energy of the incident cluster. It was observed that the spread in data points can be reduced if the yield Y and initial projectile cluster kinetic energy E are expressed in quantities scaled by the number of cluster atoms n, that is, Y/n versus E/n. The convergence of the data points is, however, not perfect, especially when the results for molecular and atomic solids are compared. In addition, the physics underlying the apparent universal dependence in not fully understood. For the study presented in this Account, we performed molecular dynamics simulations of Arn cluster bombardment of molecular (benzene, octane, and β-carotene) and atomic (Ag) solids in order to address the physical basis of the apparent universal dependence. We have demonstrated that the convergence of the data points between molecular and atomic solids can be improved if the binding energy of the solid U0 is included and the dependence is presented as Y/(E/U0) versus (E/U0)/n. As a material property, the quantity U0 is defined per the basic unit of material, which is an atom for atomic solids and a molecule for molecular solids. Analogously, the quantity Y is given in atoms and molecules, respectively. The simulations show that, for almost 3 orders of magnitude variation of (E/U0)/n, there are obvious similarities in the ejection mechanisms between the molecular and atomic solids, thus supporting the concept of universality. For large (E/U0)/n values, the mechanism of ejection is the fluid flow from a cone-shaped volume. This regime of (E/U0)/n is generally accessed experimentally by clusters with hundreds of atoms and results in the largest yields. For molecular systems, a large fraction of the total energy E is consumed by internal excitation and molecular fragmentation, which are energy loss channels not present in atomic solids. For small (E/U0)/n values, the cluster deforms the surface and the ejection occurs from a ring-shaped ridge of the forming crater rim. This regime of (E/U0)/n is generally accessed experimentally by clusters with thousands of atoms and results in the smallest yields. For the molecular systems, there is little or no molecular fragmentation. The simulations indicate, however, that the representation which includes U0 as the only material property cannot be completely universal, because there are other material properties which influence the sputtering efficiency. Furthermore, neither the Y/n nor Y/(E/U0) representation includes the energy loss physics associated with molecular fragmentation in the high (E/U0)/n regime. The analysis of the universal concept implies for practical applications that if the objective of the experiment is large material removal, then the high energy per cluster atom regime is applicable. If the objective is little or no molecular fragmentation in organic materials, then the low energy per atom regime is appropriate.
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http://dx.doi.org/10.1021/acs.accounts.5b00303DOI Listing
September 2015

Oscillations in the stability of consecutive chemical bonds revealed by ion-induced desorption.

Angew Chem Int Ed Engl 2015 Jan 4;54(4):1336-40. Epub 2014 Dec 4.

Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, 30059 Kraków (Poland).

While it is a common concept in chemistry that strengthening of one bond results in weakening of the adjacent ones, no results have been published on if and how this effect protrudes further into the molecular backbone. By binding molecules to a surface in the form of a self-assembled monolayer, the strength of a primary bond can be selectively altered. Herein, we report that by using secondary-ion mass spectrometry, we are able to detect for the first time positional oscillations in the stability of consecutive bonds along the adsorbed molecule, with the amplitudes diminishing with increasing distance from the molecule-metal interface. To explain these observations, we have performed molecular dynamics simulations and DFT calculations. These show that the oscillation effects in chemical-bond stability have a very general nature and break the translational symmetry in molecules.
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http://dx.doi.org/10.1002/anie.201406053DOI Listing
January 2015

Computed molecular depth profile for C60 bombardment of a molecular solid.

Anal Chem 2013 Dec 18;85(23):11628-33. Epub 2013 Nov 18.

Department of Chemistry, Penn State University , 104 Chemistry Building, University Park, Pennsylvania 16802, United States.

Molecular dynamics (MD) simulations have been performed for 10 keV C60 bombardment of an octane molecular solid at normal incidence. The results are analyzed using the steady-state statistical sputtering model (SS-SSM) to understand the nature of molecular motions and to predict a depth profile of a δ-layer. The octane system has sputtering yield of ~150 nm(3) of which 85% is in intact molecules and 15% is fragmented species. The main displacement mechanism is along the crater edge. Displacements between layers beneath the impact point are difficult because the nonspherically shaped octane molecule needs a relatively large volume to move into and the molecule needs to be aligned properly for the displacement. Since interlayer mixing is difficult, the predicted depth profile is dominated by the rms roughness and the large information depth because of the large sputtering yield.
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http://dx.doi.org/10.1021/ac403035aDOI Listing
December 2013

Dynamics displayed by energetic C60 bombardment of metal overlayers on an organic substrate.

Anal Chem 2013 Feb 28;85(4):2348-55. Epub 2013 Jan 28.

Department of Chemistry, 104 Chemistry Building, Pennsylvania State University, University Park, Pennsylvania 16802, United States.

Cluster bombardments of 15 keV C(60) on metal-organic interfaces composed of silver atoms and octatetraene molecules were modeled using molecular dynamics computer simulations. Dynamics revealed by the simulations include the formation of holes in the metal overlayers from which underlying organic molecules are sputtered predominantly by a rapid jetlike motion and the implantation of metal atoms and clusters in the underlying organic solid. Both of these processes negatively affect the information depth for cluster bombardment of metal-organic interfaces; therefore, the simulations presented here give a clear picture of the issues associated with depth profiling through metal-organic interfaces.
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http://dx.doi.org/10.1021/ac303348yDOI Listing
February 2013

An experimental and theoretical view of energetic C cluster bombardment onto molecular solids.

Surf Interface Anal 2013 Jan;45(1):50-53

The Pennsylvania State University, Department of Chemistry, University Park, PA, 16802, USA.

Recent experimental measurements and calculations performed by molecular dynamics computer simulations indicate, for highly energetic C 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 C 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 C 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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http://dx.doi.org/10.1002/sia.5077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547361PMC
January 2013

Partnering analytic models and dynamic secondary ion mass spectrometry simulations to interpret depth profiles due to kiloelectronvolt cluster bombardment.

Anal Chem 2012 Mar 7;84(6):3010-6. Epub 2012 Mar 7.

Smoluchowski Institute of Physics, Jagiellonian University, Kraków, Poland.

The analytical steady-state statistical sputtering model (SS-SSM) is utilized to interpret molecular dynamics (MD) simulations of depth profiling of Ag solids with keV cluster beams of C(60) and Au(3) under different incident energy and angle conditions. Specifically, the results of the MD simulations provide the input to the SS-SSM and the result is a depth profile of a delta layer. It has been found that the rms roughness of each system correlates with the total displacement yield, a new quantity introduced in this study that follows naturally from the SS-SSM. The results indicate that the best depth profiles occur when the displacement yield is low and the sputtering yield is high. Moreover, it is determined that the expected value of the delta layer position as calculated from a depth profile rather than the peak position in the depth profile is the best indicator of the actual delta layer position.
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http://dx.doi.org/10.1021/ac300363jDOI Listing
March 2012

Fluid Flow and Effusive Desorption: Dominant Mechanisms of Energy Dissipation after Energetic Cluster Bombardment of Molecular Solids.

J Phys Chem Lett 2011 Jul;2(16):2009-2014

The Pennsylvania State University, Department of Chemistry, University Park, PA 16802, USA

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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http://dx.doi.org/10.1021/jz200708jDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158660PMC
July 2011

Odd-even effects in ion-beam-induced desorption of biphenyl-substituted alkanethiol self-assembled monolayers.

Chemphyschem 2011 Jan 8;12(1):140-4. Epub 2010 Dec 8.

Laboratory of Solid State Physics and Magnetism, K.U. Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium.

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http://dx.doi.org/10.1002/cphc.201000610DOI Listing
January 2011

Internal energy of molecules ejected due to energetic C60 bombardment.

Anal Chem 2009 Mar;81(6):2260-7

Department of Chemistry, 104 Chemistry Building, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

The early stages of C(60) bombardment of octane and octatetraene crystals are modeled using molecular dynamics simulations with incident energies of 5-20 keV. Using the AIREBO potential, which allows for chemical reactions in hydrocarbon molecules, we are able to investigate how the projectile energy is partitioned into changes in potential and kinetic energy as well as how much energy flows into reacted molecules and internal energy. Several animations have been included to illustrate the bombardment process. The results show that the material near the edge of the crater can be ejected with low internal energies and that ejected molecules maintain their internal energies in the plume, in contrast to a collisional cooling mechanism previously proposed. In addition, a single C(60) bombardment was able to create many free and reacted H atoms which may aid in the ionization of molecules upon subsequent bombardment events.
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http://dx.doi.org/10.1021/ac802399mDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666284PMC
March 2009

Computational view of surface based organic mass spectrometry.

Mass Spectrom Rev 2008 Jul-Aug;27(4):289-315

Department of Chemistry, Penn State University, 104 Chemistry Building, University Park, Pennsylvania 16802, USA.

Surface based mass spectrometric approaches fill an important niche in the mass analysis portfolio of tools. The particular niche depends on both the underlying physics and chemistry of molecule ejection as well as experimental characteristics. In this article, we use molecular dynamics computer simulations to elucidate the fundamental processes giving rise to ejection of organic molecules in atomic and cluster secondary ion mass spectrometry (SIMS), massive cluster impact (MCI) mass spectrometry, and matrix-assisted laser desorption ionization (MALDI) mass spectrometry. This review is aimed at graduate students and experimental researchers.
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http://dx.doi.org/10.1002/mas.20165DOI Listing
July 2008

Microscopic insights into the sputtering of thin organic films on Ag{111} induced by C60 and Ga bombardment.

J Phys Chem B 2005 Jun;109(24):11973-9

Smoluchowski Institute of Physics, Jagiellonian University, Krakow, Poland.

Molecular dynamics computer simulations have been employed to model the bombardment of Ag{111} covered with three layers of C6H6 by 15 keV Ga and C60 projectiles. The study is aimed toward examining the mechanism by which molecules are desorbed from surfaces by energetic cluster ion beams and toward elucidating the differences between cluster bombardment and atom bombardment. The results show that the impact of the cluster on the benzene-covered surface leads to molecular desorption during the formation of a mesoscopic scale impact crater via a catapulting mechanism. Because of the high yield of C6H6 with both Ga and C60, the yield enhancement is observed to be consistent with related experimental observations. Specific energy and angle distributions are shown to be associated with the catapult mechanism.
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http://dx.doi.org/10.1021/jp050821wDOI Listing
June 2005

Enhancement of sputtering yields due to C60 versus Ga bombardment of Ag[111] as explored by molecular dynamics simulations.

Anal Chem 2003 Sep;75(17):4402-7

Smoluchowski Institute of Physics, Jagiellonian University, Krakow, Poland.

The mechanism of enhanced desorption initiated by 15-keV C60 cluster ion bombardment of a Ag single crystal surface is examined using molecular dynamics computer simulations. The size of the model microcrystallite of 165,000 atoms and the sophistication of the interaction potential function yields data that should be directly comparable with experiment. The C60 model was chosen since this source is now being used in secondary ion mass spectrometry experiments in many laboratories. The results show that a crater is formed on the Ag surface that is approximately 10 nm in diameter, a result very similar to that found for Au3 bombardment of Au. The yield of Ag atoms is approximately 16 times larger than for corresponding atomic bombardment with 15-keV Ga atoms, and the yield of Ag3 is enhanced by a factor of 35. The essential mechanistic reasons for these differences is that the C60 kinetic energy is deposited closer to the surface, with the deeply penetrating energy propagation occurring via a nondestructive pressure wave. The numbers predicted by the model are testable by experiment, and the approach is extendable to include the study of organic overlayers on metals, a situation of growing importance to the SIMS community.
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http://dx.doi.org/10.1021/ac034387aDOI Listing
September 2003