1
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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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2
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Paruch RJ, Garrison BJ, Postawa Z. Computed Molecular Depth Profile for C60 Bombardment of a Molecular solid. Anal Chem 2013; 85:11628-33. [DOI: 10.1021/ac403035a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Robert J. Paruch
- Department
of Chemistry, Penn State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
| | - Barbara J. Garrison
- Department
of Chemistry, Penn State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
| | - Zbigniew Postawa
- Smoluchowski
Institute of Physics, Jagiellonian University, ul. Reymonta 4, 30-059 Krakow, Poland
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3
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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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4
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Delcorte A, Garrison BJ, Hamraoui K. Sputtering soft materials with molecular projectiles: a microscopic view. SURF INTERFACE ANAL 2010. [DOI: 10.1002/sia.3405] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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5
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Toton D, Lorenz CD, Rompotis N, Martsinovich N, Kantorovich L. Temperature control in molecular dynamic simulations of non-equilibrium processes. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:074205. [PMID: 21386383 DOI: 10.1088/0953-8984/22/7/074205] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Thermostats are often used in various condensed matter problems, e.g. when a biological molecule undergoes a transformation in a solution, a crystal surface is irradiated with energetic particles, a crack propagates in a solid upon applied stress, two surfaces slide with respect to each other, an excited local phonon dissipates its energy into a crystal bulk, and so on. In all of these problems, as well as in many others, there is an energy transfer between different local parts of the entire system kept at a constant temperature. Very often, when modelling such processes using molecular dynamics simulations, thermostatting is done using strictly equilibrium approaches serving to describe the NVT ensemble. In this paper we critically discuss the applicability of such approaches to non-equilibrium problems, including those mentioned above, and stress that the correct temperature control can only be achieved if the method is based on the generalized Langevin equation (GLE). Specifically, we emphasize that a meaningful compromise between computational efficiency and a physically appropriate implementation of the NVT thermostat can be achieved, at least for solid state and surface problems, if the so-called stochastic boundary conditions (SBC), recently derived from the GLE (Kantorovich and Rompotis 2008 Phys. Rev. B 78 094305), are used. For SBC, the Langevin thermostat is only applied to the outer part of the simulated fragment of the entire system which borders the surrounding environment (not considered explicitly) serving as a heat bath. This point is illustrated by comparing the performance of the SBC and some of the equilibrium thermostats in two problems: (i) irradiation of the Si(001) surface with an energetic CaF(2) molecule using an ab initio density functional theory based method, and (ii) the tribology of two amorphous SiO(2) surfaces coated with self-assembled monolayers of methyl-terminated hydrocarbon alkoxylsilane molecules using a classical atomistic force field. We discuss the differences in behaviour of these systems due to applied thermostatting, and show that in some cases a qualitatively different physical behaviour of the simulated system can be obtained if an equilibrium thermostat is used.
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Affiliation(s)
- Dawid Toton
- Physics, King's College London, The Strand, London WC2R 2LS, UK
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6
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Delcorte A, Garrison BJ, Hamraoui K. Dynamics of Molecular Impacts on Soft Materials: From Fullerenes to Organic Nanodrops. Anal Chem 2009; 81:6676-86. [DOI: 10.1021/ac900746x] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A. Delcorte
- Unité PCPM, Université Catholique de Louvain, 1 Croix du Sud, B-1348, Louvain-la-Neuve, Belgium, and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - B. J. Garrison
- Unité PCPM, Université Catholique de Louvain, 1 Croix du Sud, B-1348, Louvain-la-Neuve, Belgium, and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - K. Hamraoui
- Unité PCPM, Université Catholique de Louvain, 1 Croix du Sud, B-1348, Louvain-la-Neuve, Belgium, and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
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7
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Armata N, Baldissin G, Barone G, Cortese R, D’Anna V, Ferrante F, Giuffrida S, Li Manni G, Prestianni A, Rubino T, Varga Z, Duca D. Molecular-Level Characterization of Heterogeneous Catalytic Systems by Algorithmic Time Dependent Monte Carlo. Top Catal 2009. [DOI: 10.1007/s11244-008-9178-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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8
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Garrison BJ, Postawa Z. Computational view of surface based organic mass spectrometry. MASS SPECTROMETRY REVIEWS 2008; 27:289-315. [PMID: 18421766 DOI: 10.1002/mas.20165] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
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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Affiliation(s)
- Barbara J Garrison
- Department of Chemistry, Penn State University, 104 Chemistry Building, University Park, Pennsylvania 16802, USA.
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9
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Smiley EJ, Winograd N, Garrison BJ. Effect of cluster size in kiloelectronvolt cluster bombardment of solid benzene. Anal Chem 2007; 79:494-9. [PMID: 17222012 DOI: 10.1021/ac061531u] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Emission of benzene molecules by 5-keV cluster bombardment of a range of carbon projectiles from C6H6 to C180 is studied by a coarse-grained molecular dynamics (MD) technique. This approach permits calculations that are not feasible using more complicated potential energy functions, particularly as the interesting physics associated with the ion impact event approaches the mesoscale. These calculations show that the highest ejection yields are associated with clusters that deposit their incident energy 15-20 A below the surface. The highest yield for the projectiles is produced by the C20 and C60 projectiles. The results from the MD simulations are also compared favorably to an analytical model based on fluid dynamics to describe the energy deposition. The analytical model is then utilized to extend the range of the calculations to higher incident energies. The issue of the relative amount of chemical fragmentation and intact molecular desorption is also examined for the benzene crystal. These results show that damage accumulation at high-incident fluence should not be problematic and that it should be possible to perform molecular depth profiling via secondary ion mass spectrometry experiments. In general, the approach presented here illustrates the power of combining a simplified MD method with analytical strategies for describing a length scale that is difficult to achieve with traditional MD calculations.
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Affiliation(s)
- Edward J Smiley
- Department of Chemistry, 104 Chemistry Building, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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10
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Duca D, Barone G, Giuffrida S, Varga Z. IDEA: Interface dynamics and energetics algorithm. J Comput Chem 2007; 28:2483-99. [PMID: 17721923 DOI: 10.1002/jcc.20722] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
IDEA, interface dynamics and energetics algorithm, was implemented, in FORTRAN, under different operating systems to mimic dynamics and energetics of elementary events involved in interfacial processes. The code included a parallel elaboration scheme in which both the stochastic and the deterministic components, involved in the developed physical model, worked simultaneously. IDEA also embodied an optionally running VISUAL subroutine, showing the dynamic energy changes caused by the surface events, e.g., occurring at the gas-solid interface. Monte Carlo and ordinary differential equation system subroutines were employed in a synergistic way to drive the occurrence of the elementary events and to manage the implied energy flows, respectively. Biphase processes, namely isothermal and isobaric adsorption of carbon monoxide on nickel, palladium, and platinum surfaces, were first studied to test the capability of the code in modeling real frames. On the whole, the simulated results showed that IDEA could reproduce the inner characteristics of the studied systems and predict properties not yet experimentally investigated.
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Affiliation(s)
- D Duca
- Dipartimento di Chimica Inorganica e Analitica Stanislao Cannizzaro dell'Università, viale delle Scienze, parco d'Orleans II, I-90128 Palermo, Sicily, Italy.
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11
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Wojciechowski IA, Garrison BJ. Sputtering of Water Ice Induced by C60 Bombardment: Onset of Plume Formation. J Phys Chem A 2005; 110:1389-92. [PMID: 16435799 DOI: 10.1021/jp054512h] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interaction of a 5 keV C(60) projectile with amorphous water ice is studied using molecular dynamics computer simulations. The energetic C(60) molecule causes large-scale collisional events in the subsurface region, involving more than 10(4) water molecules in a time of less than 3 ps. The energy deposited in the sample is sufficiently large to turn the ice into a superheated and superdense gas. The gas is expelled into the vacuum, leading to the formation of a flow that manifests itself in the angular and velocity distributions of emitted water molecules.
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Affiliation(s)
- I A Wojciechowski
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, USA
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12
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Postawa Z, Czerwinski B, Winograd N, Garrison BJ. Microscopic Insights into the Sputtering of Thin Organic Films on Ag{111} Induced by C60 and Ga Bombardment. J Phys Chem B 2005; 109:11973-9. [PMID: 16852476 DOI: 10.1021/jp050821w] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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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Affiliation(s)
- Zbigniew Postawa
- Smoluchowski Institute of Physics, Jagiellonian University, Krakow, Poland.
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13
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Delcorte A, Garrison BJ. Kiloelectronvolt Argon-Induced Molecular Desorption from a Bulk Polystyrene Solid. J Phys Chem B 2004. [DOI: 10.1021/jp0402131] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Troya * D, Schatz † GC. Hyperthermal chemistry in the gas phase and on surfaces: theoretical studies. INT REV PHYS CHEM 2004. [DOI: 10.1080/0144235042000298484] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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15
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Akin FA, Jang I, Schlossman ML, Sinnott SB, Zajac G, Fuoco ER, Wijesundara MBJ, Li M, Tikhonov A, Pingali SV, Wroble AT, Hanley L. Nanostructure of Fluorocarbon Films Deposited on Polystyrene from Hyperthermal C3F5+ Ions. J Phys Chem B 2004. [DOI: 10.1021/jp036129n] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- F. Ahu Akin
- Departments of Chemistry and Physics, University of Illinois at Chicago, Chicago, Illinois 60607-7061, Department Materials Science & Engineering, University of Florida, Gainesville, Florida 32611-6400, and BP Chemicals Research Center, 150 W. Warrenville Road., Naperville, Illinois 60566
| | - Inkook Jang
- Departments of Chemistry and Physics, University of Illinois at Chicago, Chicago, Illinois 60607-7061, Department Materials Science & Engineering, University of Florida, Gainesville, Florida 32611-6400, and BP Chemicals Research Center, 150 W. Warrenville Road., Naperville, Illinois 60566
| | - Mark L. Schlossman
- Departments of Chemistry and Physics, University of Illinois at Chicago, Chicago, Illinois 60607-7061, Department Materials Science & Engineering, University of Florida, Gainesville, Florida 32611-6400, and BP Chemicals Research Center, 150 W. Warrenville Road., Naperville, Illinois 60566
| | - Susan B. Sinnott
- Departments of Chemistry and Physics, University of Illinois at Chicago, Chicago, Illinois 60607-7061, Department Materials Science & Engineering, University of Florida, Gainesville, Florida 32611-6400, and BP Chemicals Research Center, 150 W. Warrenville Road., Naperville, Illinois 60566
| | - Gerry Zajac
- Departments of Chemistry and Physics, University of Illinois at Chicago, Chicago, Illinois 60607-7061, Department Materials Science & Engineering, University of Florida, Gainesville, Florida 32611-6400, and BP Chemicals Research Center, 150 W. Warrenville Road., Naperville, Illinois 60566
| | - Erick R. Fuoco
- Departments of Chemistry and Physics, University of Illinois at Chicago, Chicago, Illinois 60607-7061, Department Materials Science & Engineering, University of Florida, Gainesville, Florida 32611-6400, and BP Chemicals Research Center, 150 W. Warrenville Road., Naperville, Illinois 60566
| | - Muthu B. J. Wijesundara
- Departments of Chemistry and Physics, University of Illinois at Chicago, Chicago, Illinois 60607-7061, Department Materials Science & Engineering, University of Florida, Gainesville, Florida 32611-6400, and BP Chemicals Research Center, 150 W. Warrenville Road., Naperville, Illinois 60566
| | - Ming Li
- Departments of Chemistry and Physics, University of Illinois at Chicago, Chicago, Illinois 60607-7061, Department Materials Science & Engineering, University of Florida, Gainesville, Florida 32611-6400, and BP Chemicals Research Center, 150 W. Warrenville Road., Naperville, Illinois 60566
| | - Aleksey Tikhonov
- Departments of Chemistry and Physics, University of Illinois at Chicago, Chicago, Illinois 60607-7061, Department Materials Science & Engineering, University of Florida, Gainesville, Florida 32611-6400, and BP Chemicals Research Center, 150 W. Warrenville Road., Naperville, Illinois 60566
| | - Sai Venkatesh Pingali
- Departments of Chemistry and Physics, University of Illinois at Chicago, Chicago, Illinois 60607-7061, Department Materials Science & Engineering, University of Florida, Gainesville, Florida 32611-6400, and BP Chemicals Research Center, 150 W. Warrenville Road., Naperville, Illinois 60566
| | - Amanda T. Wroble
- Departments of Chemistry and Physics, University of Illinois at Chicago, Chicago, Illinois 60607-7061, Department Materials Science & Engineering, University of Florida, Gainesville, Florida 32611-6400, and BP Chemicals Research Center, 150 W. Warrenville Road., Naperville, Illinois 60566
| | - Luke Hanley
- Departments of Chemistry and Physics, University of Illinois at Chicago, Chicago, Illinois 60607-7061, Department Materials Science & Engineering, University of Florida, Gainesville, Florida 32611-6400, and BP Chemicals Research Center, 150 W. Warrenville Road., Naperville, Illinois 60566
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16
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Postawa Z, Czerwinski B, Szewczyk M, Smiley EJ, Winograd N, Garrison BJ. Microscopic Insights into the Sputtering of Ag{111} Induced by C60and Ga Bombardment. J Phys Chem B 2004. [DOI: 10.1021/jp049936a] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Postawa Z, Czerwinski B, Szewczyk M, Smiley EJ, Winograd N, Garrison BJ. Enhancement of Sputtering Yields Due to C60versus Ga Bombardment of Ag{111} As Explored by Molecular Dynamics Simulations. Anal Chem 2003; 75:4402-7. [PMID: 14632043 DOI: 10.1021/ac034387a] [Citation(s) in RCA: 171] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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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Affiliation(s)
- Zbigniew Postawa
- Smoluchowski Institute of Physics, Jagiellonian University, Krakow, Poland.
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18
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Dou Y, Winograd N, Garrison BJ, Zhigilei LV. Substrate-Assisted Laser-Initiated Ejection of Proteins Embedded in Water Films. J Phys Chem B 2003. [DOI: 10.1021/jp0267306] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yusheng Dou
- Department of Physics, Texas A&M University, College Station, Texas 77843, Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, and Department of Materials Science and Engineering, University of Virginia, Charlottesville, Virginia 22903
| | - Nicholas Winograd
- Department of Physics, Texas A&M University, College Station, Texas 77843, Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, and Department of Materials Science and Engineering, University of Virginia, Charlottesville, Virginia 22903
| | - Barbara J. Garrison
- Department of Physics, Texas A&M University, College Station, Texas 77843, Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, and Department of Materials Science and Engineering, University of Virginia, Charlottesville, Virginia 22903
| | - Leonid V. Zhigilei
- Department of Physics, Texas A&M University, College Station, Texas 77843, Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, and Department of Materials Science and Engineering, University of Virginia, Charlottesville, Virginia 22903
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19
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Wojciechowski I, Medvedeva M, Garrison BJ, Ferleger VK, Heiland W. Dissociative Grazing Scattering of H2+ Ions from Metal Surfaces. J Phys Chem B 2002. [DOI: 10.1021/jp020671e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Igor Wojciechowski
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, Arifov Institute of Electronics, Tashkent 700143, Uzbekistan and Fachbereich Physik, Universität Osnabrück, Barbarastr. 7, D-49069 Osnabrück, Germany
| | - Marina Medvedeva
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, Arifov Institute of Electronics, Tashkent 700143, Uzbekistan and Fachbereich Physik, Universität Osnabrück, Barbarastr. 7, D-49069 Osnabrück, Germany
| | - Barbara J. Garrison
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, Arifov Institute of Electronics, Tashkent 700143, Uzbekistan and Fachbereich Physik, Universität Osnabrück, Barbarastr. 7, D-49069 Osnabrück, Germany
| | - Vladimir K. Ferleger
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, Arifov Institute of Electronics, Tashkent 700143, Uzbekistan and Fachbereich Physik, Universität Osnabrück, Barbarastr. 7, D-49069 Osnabrück, Germany
| | - Werner Heiland
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, Arifov Institute of Electronics, Tashkent 700143, Uzbekistan and Fachbereich Physik, Universität Osnabrück, Barbarastr. 7, D-49069 Osnabrück, Germany
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20
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Hydrogenation of light hydrocarbons on palladium: theoretical study of the local surface arrangements. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0166-1280(00)00843-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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21
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Dou Y, Zhigilei LV, Winograd N, Garrison BJ. Explosive Boiling of Water Films Adjacent to Heated Surfaces: A Microscopic Description. J Phys Chem A 2001. [DOI: 10.1021/jp003913o] [Citation(s) in RCA: 155] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yusheng Dou
- Department of Chemistry and Materials Research Institute, Penn State University, University Park, Pennsylvania 16802, and Department of Materials Science and Engineering, University of Virginia, Charlottesville, Virginia 22903
| | - Leonid V. Zhigilei
- Department of Chemistry and Materials Research Institute, Penn State University, University Park, Pennsylvania 16802, and Department of Materials Science and Engineering, University of Virginia, Charlottesville, Virginia 22903
| | - Nicholas Winograd
- Department of Chemistry and Materials Research Institute, Penn State University, University Park, Pennsylvania 16802, and Department of Materials Science and Engineering, University of Virginia, Charlottesville, Virginia 22903
| | - Barbara J. Garrison
- Department of Chemistry and Materials Research Institute, Penn State University, University Park, Pennsylvania 16802, and Department of Materials Science and Engineering, University of Virginia, Charlottesville, Virginia 22903
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22
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Brown RC, Roberts JT. Microstructure Evolution in Diamond CVD: Computer Simulations of 111 Surface Site Formation on a Growing Diamond-100 Surface. J Phys Chem B 2000. [DOI: 10.1021/jp000978i] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ronald C. Brown
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Jeffrey T. Roberts
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455-0431
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Nguyen TC, Ward DW, Townes JA, White AK, Krantzman KD, Garrison BJ. A Theoretical Investigation of the Yield-to-Damage Enhancement with Polyatomic Projectiles in Organic SIMS. J Phys Chem B 2000. [DOI: 10.1021/jp001089y] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Abstract
Molecular dynamics simulations have been used to model the kiloelectronvolt particle bombardment of organic layers on metal substrates such as occurs in the analytical techniques of secondary ion mass spectrometry and fast atom bombardment mass spectrometry. Vignettes of insights gained from the simulations along with comparisons to experimental data are presented in this Account. Topics include intact molecular ejection vs fragmentation, prediction of reaction pathways, influence of the substrate, and quantitative predictions of energy and angular distributions.
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Affiliation(s)
- B J Garrison
- Department of Chemistry, Penn State University, University Park, PA 16802, USA
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25
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Hanley L, Kornienko O, Ada ET, Fuoco E, Trevor JL. Surface mass spectrometry of molecular species. JOURNAL OF MASS SPECTROMETRY : JMS 1999; 34:705-723. [PMID: 10407355 DOI: 10.1002/(sici)1096-9888(199907)34:7<705::aid-jms845>3.0.co;2-b] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
This tutorial discusses the predominant methods available for surface mass spectrometry (MS) of molecular species: thermal desorption spectroscopy, laser desorption MS, secondary ion MS, post-ionization of desorbed neutrals and surface matrix-assisted laser desorption/ionization. Each of these has the capability to analyze molecular species that are chemisorbed, physisorbed, covalently bound to or the predominant component of a solid surface. These surface MS methods are briefly described, then their capabilities demonstrated using data predominantly from the authors' work. Comparisons are made with related methods in conventional MS. A very brief discussion is provided on the importance of complementing surface MS data with data from x-ray photoelectron spectroscopy and other surface analysis tools.
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Affiliation(s)
- L Hanley
- Department of Chemistry, m/c 111, University of Illinois at Chicago, 845 W. Taylor St., 4500 SES, Chicago, Illinois 60607-7061, USA.
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Liu KSS, Yong CW, Garrison BJ, Vickerman JC. Molecular Dynamics Simulations of Particle Bombardment Induced Desorption Processes: Alkanethiolates on Au(111). J Phys Chem B 1999. [DOI: 10.1021/jp984071k] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- K. S. S. Liu
- Surface Analysis Research Centre, Department of Chemistry, UMIST, PO Box 88, Manchester, M60 1QD, U.K., School of Biological Sciences, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, U.K., and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - C. W. Yong
- Surface Analysis Research Centre, Department of Chemistry, UMIST, PO Box 88, Manchester, M60 1QD, U.K., School of Biological Sciences, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, U.K., and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - B. J. Garrison
- Surface Analysis Research Centre, Department of Chemistry, UMIST, PO Box 88, Manchester, M60 1QD, U.K., School of Biological Sciences, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, U.K., and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - J. C. Vickerman
- Surface Analysis Research Centre, Department of Chemistry, UMIST, PO Box 88, Manchester, M60 1QD, U.K., School of Biological Sciences, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, U.K., and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
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27
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Chatterjee R, Postawa Z, Winograd N, Garrison BJ. Molecular Dynamics Simulation Study of Molecular Ejection Mechanisms: keV Particle Bombardment of C6H6/Ag{111}. J Phys Chem B 1999. [DOI: 10.1021/jp9833045] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Kubo M, Oumi Y, Miura R, Stirling A, Miyamoto A, Kawasaki M, Yoshimoto M, Koinuma H. Molecular dynamics simulation on a layer-by-layer homoepitaxial growth process of SrTiO3(001). J Chem Phys 1998. [DOI: 10.1063/1.477525] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Feng B, Shen J, Grill V, Evans C, Cooks RG. Cleavage of C−C and C−F Bonds by Xe+• and I+ Ions in Reactions at a Fluorinated Self-Assembled Monolayer Surface: Collision Energy Dependence and Mechanisms. J Am Chem Soc 1998. [DOI: 10.1021/ja973201k] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- B. Feng
- Contribution from the Department of Chemistry, Purdue University, West Lafayette, Indiana 47907
| | - J. Shen
- Contribution from the Department of Chemistry, Purdue University, West Lafayette, Indiana 47907
| | - V. Grill
- Contribution from the Department of Chemistry, Purdue University, West Lafayette, Indiana 47907
| | - C. Evans
- Contribution from the Department of Chemistry, Purdue University, West Lafayette, Indiana 47907
| | - R. G. Cooks
- Contribution from the Department of Chemistry, Purdue University, West Lafayette, Indiana 47907
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Mahaffy R, Bhatia R, Garrison BJ. Diffusion of a Butanethiolate Molecule on a Au{111} Surface. J Phys Chem B 1997. [DOI: 10.1021/jp962281w] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rachel Mahaffy
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Reena Bhatia
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Barbara J. Garrison
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
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32
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Wucher A, Garrison BJ. Cluster formation in sputtering: A molecular dynamics study using the MD/MC‐corrected effective medium potential. J Chem Phys 1996. [DOI: 10.1063/1.472451] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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