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Gu M, Yang L, Hase WL, Sun J, Zhang J. Energy Transfer of Peptide Ions Colliding with a Self‐Assembled Monolayer Surface. The Influence of Peptide Ion Size. CHINESE J CHEM 2019. [DOI: 10.1002/cjoc.201800544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Meng Gu
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology Harbin Heilongjiang 150001 China
| | - Li Yang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology Harbin Heilongjiang 150001 China
| | - William L Hase
- Department of Chemistry and BiochemistryTexas Tech University Lubbock TX 79401 USA
| | - Jianmin Sun
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology Harbin Heilongjiang 150001 China
| | - Jiaxu Zhang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology Harbin Heilongjiang 150001 China
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2
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Frederickson D, McDonough M, Barnes GL. A Computational Comparison of Soft Landing of α-Helical vs Globular Peptides. J Phys Chem B 2018; 122:9549-9554. [DOI: 10.1021/acs.jpcb.8b06232] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Danielle Frederickson
- Department of Chemistry and Biochemistry, Siena College, 515 Loudon Road, Loudonville, New York 12211, United States
| | - Meghan McDonough
- Department of Chemistry and Biochemistry, Siena College, 515 Loudon Road, Loudonville, New York 12211, United States
| | - George L. Barnes
- Department of Chemistry and Biochemistry, Siena College, 515 Loudon Road, Loudonville, New York 12211, United States
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3
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Ross-Naylor JA, Mijajlovic M, Zhang H, Biggs MJ. Characterizing the Switching Transitions of an Adsorbed Peptide by Mapping the Potential Energy Surface. J Phys Chem B 2017; 121:11455-11464. [DOI: 10.1021/acs.jpcb.7b10319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- James A. Ross-Naylor
- School of Chemical Engineering, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Milan Mijajlovic
- School of Chemical Engineering, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Hu Zhang
- School of Chemical Engineering, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Mark J. Biggs
- School of Chemical Engineering, The University of Adelaide, Adelaide, South Australia 5005, Australia
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Pratihar S, Barnes GL, Laskin J, Hase WL. Dynamics of Protonated Peptide Ion Collisions with Organic Surfaces: Consonance of Simulation and Experiment. J Phys Chem Lett 2016; 7:3142-3150. [PMID: 27467857 DOI: 10.1021/acs.jpclett.6b00978] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In this Perspective, mass spectrometry experiments and chemical dynamics simulations are described that have explored the atomistic dynamics of protonated peptide ions, peptide-H(+), colliding with organic surfaces. These studies have investigated the energy transfer and fragmentation dynamics for peptide-H(+) surface-induced dissociation (SID), peptide-H(+) physisorption on the surface, soft landing (SL), and peptide-H(+) reaction with the surface, reactive landing (RL). SID provides primary structures of biological ions and information regarding their fragmentation pathways and energetics. Two SID mechanisms are found for peptide-H(+) fragmentation. A traditional mechanism in which peptide-H(+) is vibrationally excited by its collision with the surface, rebounds off the surface and then dissociates in accord with the statistical, RRKM unimolecular rate theory. The other, shattering, is a nonstatistical mechanism in which peptide-H(+) fragments as it collides with the surface, dissociating via many pathways and forming many product ions. Shattering is important for collisions with diamond and perfluorinated self-assembled monolayer (F-SAM) surfaces, increasing in importance with the peptide-H(+) collision energy. Chemical dynamics simulations also provide important mechanistic insights on SL and RL of biological ions on surfaces. The simulations indicate that SL occurs via multiple mechanisms consisting of sequences of peptide-H(+) physisorption on and penetration in the surface. SL and RL have a broad range of important applications including preparation of protein or peptide microarrays, development of biocompatible substrates and biosensors, and preparation of novel synthetic materials, including nanomaterials. An important RL mechanism is intact deposition of peptide-H(+) on the surface.
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Affiliation(s)
- Subha Pratihar
- Department of Chemistry and Biochemistry, Texas Tech University , Lubbock, Texas 79409-1061, United States
| | - George L Barnes
- Department of Chemistry and Biochemistry, Siena College , Loudonville, New York 12211, United States
| | - Julia Laskin
- Pacific Northwest National Laboratory , Physical Sciences Division, P.O. Box 999 K8-88, Richland, Washington 99352, United States
| | - William L Hase
- Department of Chemistry and Biochemistry, Texas Tech University , Lubbock, Texas 79409-1061, United States
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5
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Hu Q, Laskin J. Secondary Structures of Ubiquitin Ions Soft-Landed onto Self-Assembled Monolayer Surfaces. J Phys Chem B 2016; 120:4927-36. [DOI: 10.1021/acs.jpcb.6b02448] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Qichi Hu
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Julia Laskin
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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6
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Johnson GE, Gunaratne D, Laskin J. Soft- and reactive landing of ions onto surfaces: Concepts and applications. MASS SPECTROMETRY REVIEWS 2016; 35:439-479. [PMID: 25880894 DOI: 10.1002/mas.21451] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 10/31/2014] [Indexed: 06/04/2023]
Abstract
Soft- and reactive landing of mass-selected ions is gaining attention as a promising approach for the precisely-controlled preparation of materials on surfaces that are not amenable to deposition using conventional methods. A broad range of ionization sources and mass filters are available that make ion soft-landing a versatile tool for surface modification using beams of hyperthermal (<100 eV) ions. The ability to select the mass-to-charge ratio of the ion, its kinetic energy and charge state, along with precise control of the size, shape, and position of the ion beam on the deposition target distinguishes ion soft landing from other surface modification techniques. Soft- and reactive landing have been used to prepare interfaces for practical applications as well as precisely-defined model surfaces for fundamental investigations in chemistry, physics, and materials science. For instance, soft- and reactive landing have been applied to study the surface chemistry of ions isolated in the gas-phase, prepare arrays of proteins for high-throughput biological screening, produce novel carbon-based and polymer materials, enrich the secondary structure of peptides and the chirality of organic molecules, immobilize electrochemically-active proteins and organometallics on electrodes, create thin films of complex molecules, and immobilize catalytically active organometallics as well as ligated metal clusters. In addition, soft landing has enabled investigation of the size-dependent behavior of bare metal clusters in the critical subnanometer size regime where chemical and physical properties do not scale predictably with size. The morphology, aggregation, and immobilization of larger bare metal nanoparticles, which are directly relevant to the design of catalysts as well as improved memory and electronic devices, have also been studied using ion soft landing. This review article begins in section 1 with a brief introduction to the existing applications of ion soft- and reactive landing. Section 2 provides an overview of the ionization sources and mass filters that have been used to date for soft landing of mass-selected ions. A discussion of the competing processes that occur during ion deposition as well as the types of ions and surfaces that have been investigated follows in section 3. Section 4 discusses the physical phenomena that occur during and after ion soft landing, including retention and reduction of ionic charge along with factors that impact the efficiency of ion deposition. The influence of soft landing on the secondary structure and biological activity of complex ions is addressed in section 5. Lastly, an overview of the structure and mobility as well as the catalytic, optical, magnetic, and redox properties of bare ionic clusters and nanoparticles deposited onto surfaces is presented in section 6.
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Affiliation(s)
- Grant E Johnson
- Physical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN K8-88, Richland, WA, 99352
| | - Don Gunaratne
- Physical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN K8-88, Richland, WA, 99352
| | - Julia Laskin
- Physical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN K8-88, Richland, WA, 99352
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Gunaratne KDD, Prabhakaran V, Andersen A, Johnson GE, Laskin J. Charge retention of soft-landed phosphotungstate Keggin anions on self-assembled monolayers. Phys Chem Chem Phys 2016; 18:9021-8. [DOI: 10.1039/c5cp06954h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Preferential immobilization of the 2− charge state observed for polyoxotungstate Keggin anions soft-landed onto self-assembled monolayer surfaces.
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Affiliation(s)
| | | | - Amity Andersen
- Pacific Northwest National Laboratory
- Physical Sciences Division
- Richland
- USA
| | - Grant E. Johnson
- Pacific Northwest National Laboratory
- Physical Sciences Division
- Richland
- USA
| | - Julia Laskin
- Pacific Northwest National Laboratory
- Physical Sciences Division
- Richland
- USA
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8
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Gunaratne KDD, Prabhakaran V, Ibrahim YM, Norheim RV, Johnson GE, Laskin J. Design and performance of a high-flux electrospray ionization source for ion soft landing. Analyst 2015; 140:2957-63. [DOI: 10.1039/c5an00220f] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A high-flux electrospray source enables deposition of micrograms of mass-selected ions for studies in catalysis and materials science.
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Affiliation(s)
| | | | - Yehia M. Ibrahim
- Biological Sciences Division and Environmental Molecular Sciences Laboratory
- Pacific Northwest National Laboratory
- Richland
- USA
| | - Randolph V. Norheim
- Biological Sciences Division and Environmental Molecular Sciences Laboratory
- Pacific Northwest National Laboratory
- Richland
- USA
| | - Grant E. Johnson
- Pacific Northwest National Laboratory
- Physical Sciences Division
- Richland
- USA
| | - Julia Laskin
- Pacific Northwest National Laboratory
- Physical Sciences Division
- Richland
- USA
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Schubert F, Rossi M, Baldauf C, Pagel K, Warnke S, von Helden G, Filsinger F, Kupser P, Meijer G, Salwiczek M, Koksch B, Scheffler M, Blum V. Exploring the conformational preferences of 20-residue peptides in isolation: Ac-Ala19-Lys + H+vs. Ac-Lys-Ala19 + H+ and the current reach of DFT. Phys Chem Chem Phys 2015; 17:7373-85. [DOI: 10.1039/c4cp05541a] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using a high-level density functional and an exhaustive search of conformation space, the predicted conformation of a 20-amino acid peptide explains two seemingly contradictory experiments.
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Affiliation(s)
| | - Mariana Rossi
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
- Physical and Theoretical Chemistry Laboratory
- University of Oxford
| | - Carsten Baldauf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
| | - Kevin Pagel
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
- Institut für Chemie und Biochemie - Organische Chemie
- Freie Universität Berlin
| | - Stephan Warnke
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
| | - Frank Filsinger
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
| | - Peter Kupser
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
- Radboud University Nijmegen
- 65000 HC Nijmegen
| | - Mario Salwiczek
- Institut für Chemie und Biochemie - Organische Chemie
- Freie Universität Berlin
- D-14195 Berlin
- Germany
| | - Beate Koksch
- Institut für Chemie und Biochemie - Organische Chemie
- Freie Universität Berlin
- D-14195 Berlin
- Germany
| | | | - Volker Blum
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
- Department Mechanical Engineering and Material Science and Center for Materials Genomics
- Duke University
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Mikhailov VA, Mize TH, Benesch JLP, Robinson CV. Mass-selective soft-landing of protein assemblies with controlled landing energies. Anal Chem 2014; 86:8321-8. [PMID: 25026391 DOI: 10.1021/ac5018327] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Selection and soft-landing of bionanoparticles in vacuum is potentially a preparative approach to separate heterogeneous mixtures for high-resolution structural study or to deposit homogeneous materials for nanotechnological applications. Soft-landing of intact protein assemblies however remains challenging, due to the difficulties of manipulating these heavy species in mass-selective devices and retaining their structure during the experiment. We have developed a tandem mass spectrometer with the capability for controlled ion soft-landing and ex situ visualization of the soft-landed particles by means of transmission electron microscopy. The deposition conditions can be controlled by adjusting the kinetic energies of the ions by applying accelerating or decelerating voltages to a set of ion-steering optics. To validate this approach, we have examined two cage-like protein complexes, GroEL and ferritin, and studied the effect of soft-landing conditions on the method's throughput and the preservation of protein structure. Separation, based on mass-to-charge ratio, of holo- and apo-ferritin complexes after electrospray ionization enabled us to soft-land independently the separated complexes on a grid suitable for downstream transmission electron microscopy analysis. Following negative staining, images of the soft-landed complexes reveal that their structural integrity is largely conserved, with the characteristic central cavity of apoferritin, and iron core of holoferritin, surviving the phase transition from liquid to gas, soft-landing, and dehydration in vacuum.
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Affiliation(s)
- Victor A Mikhailov
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford , Oxford, OX1 3QZ, United Kingdom
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Johnson GE, Gunaratne KDD, Laskin J. In situ SIMS and IR spectroscopy of well-defined surfaces prepared by soft landing of mass-selected ions. J Vis Exp 2014:51344. [PMID: 24961913 PMCID: PMC4195338 DOI: 10.3791/51344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Soft landing of mass-selected ions onto surfaces is a powerful approach for the highly-controlled preparation of materials that are inaccessible using conventional synthesis techniques. Coupling soft landing with in situ characterization using secondary ion mass spectrometry (SIMS) and infrared reflection absorption spectroscopy (IRRAS) enables analysis of well-defined surfaces under clean vacuum conditions. The capabilities of three soft-landing instruments constructed in our laboratory are illustrated for the representative system of surface-bound organometallics prepared by soft landing of mass-selected ruthenium tris(bipyridine) dications, [Ru(bpy)3](2+) (bpy = bipyridine), onto carboxylic acid terminated self-assembled monolayer surfaces on gold (COOH-SAMs). In situ time-of-flight (TOF)-SIMS provides insight into the reactivity of the soft-landed ions. In addition, the kinetics of charge reduction, neutralization and desorption occurring on the COOH-SAM both during and after ion soft landing are studied using in situ Fourier transform ion cyclotron resonance (FT-ICR)-SIMS measurements. In situ IRRAS experiments provide insight into how the structure of organic ligands surrounding metal centers is perturbed through immobilization of organometallic ions on COOH-SAM surfaces by soft landing. Collectively, the three instruments provide complementary information about the chemical composition, reactivity and structure of well-defined species supported on surfaces.
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Affiliation(s)
- Grant E Johnson
- Physical Sciences Division, Pacific Northwest National Laboratory
| | | | - Julia Laskin
- Physical Sciences Division, Pacific Northwest National Laboratory;
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Pratihar S, Kohale SC, Vázquez SA, Hase WL. Intermolecular potential for binding of protonated peptide ions with perfluorinated hydrocarbon surfaces. J Phys Chem B 2014; 118:5577-88. [PMID: 24779856 DOI: 10.1021/jp410886s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
An analytic potential energy function was developed to model both short-range and long-range interactions between protonated peptide ions and perfluorinated hydrocarbon chains. The potential function is defined as a sum of two-body potentials of the Buckingham form. The parameters of the two-body potentials were obtained by fits to intermolecular potential energy curves (IPECs) calculated for CF4, which represents the F and C atoms of a perfluoroalkane chain, interacting with small molecules chosen as representatives of the main functional groups and atoms present in protonated peptide ions: specifically, CH4, NH3, NH4(+), and HCOOH. The IPECs were calculated at the MP2/aug-cc-pVTZ level of theory, with basis set superposition error (BSSE) corrections. Good fits were obtained for an energy range extending up to about 400 kcal/mol. It is shown that the pair potentials derived from the NH3/CF4 and HCOOH/CF4 fits reproduce acceptably well the intermolecular interactions in HCONH2/CF4, which indicates that the parameters obtained for the amine and carbonyl atoms may be transferable to the corresponding atoms of the amide group. The derived potential energy function may be used in chemical dynamics simulations of collisions of peptide-H(+) ions with perfluorinated hydrocarbon surfaces.
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Affiliation(s)
- Subha Pratihar
- Department of Chemistry and Biochemistry, Texas Tech University , Lubbock, Texas 79409-1061, United States
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13
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Rossi M, Scheffler M, Blum V. Impact of Vibrational Entropy on the Stability of Unsolvated Peptide Helices with Increasing Length. J Phys Chem B 2013; 117:5574-84. [DOI: 10.1021/jp402087e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Mariana Rossi
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Matthias Scheffler
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Volker Blum
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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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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16
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Analysis and modification of surfaces using molecular ions in the ambient environment. Curr Opin Chem Biol 2011; 15:741-7. [DOI: 10.1016/j.cbpa.2011.06.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 05/26/2011] [Accepted: 06/06/2011] [Indexed: 11/23/2022]
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Johnson GE, Hu Q, Laskin J. Soft landing of complex molecules on surfaces. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2011; 4:83-104. [PMID: 21370985 DOI: 10.1146/annurev-anchem-061010-114028] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Soft and reactive landing of mass-selected ions onto surfaces has become a topic of substantial interest due to its promising potential for the highly controlled preparation of materials. For example, there are possible applications in the production of peptide and protein microarrays for use in high-throughput screening, protein separation and conformational enrichment of peptides, redox protein characterization, thin-film production, and the preparation of catalysts through deposition of clusters and organometallic complexes. Soft landing overcomes many of the limitations associated with conventional thin-film production techniques and offers unprecedented selectivity and specificity of preparation of deposited species. This review discusses the fundamental aspects of soft and reactive landing of mass-selected ions on surfaces that pertain to applications of these techniques in biomaterials, molecular electronics, catalysis, and interfacial chemistry.
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Affiliation(s)
- Grant E Johnson
- Fundamental Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA.
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