Role of the Molecular Environment in Quenching the Irradiation-Driven Fragmentation of Fe(CO)5: A Reactive Molecular Dynamics Study

. 2023 May 04 ; 127 (17) : 3757-3767. [epub] 20230419

Status PubMed-not-MEDLINE Jazyk angličtina Země Spojené státy americké Médium print-electronic

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid37076805

Irradiation-driven fragmentation and chemical transformations of molecular systems play a key role in nanofabrication processes where organometallic compounds break up due to the irradiation with focused particle beams. In this study, reactive molecular dynamics simulations have been performed to analyze the role of the molecular environment on the irradiation-induced fragmentation of molecular systems. As a case study, we consider the dissociative ionization of iron pentacarbonyl, Fe(CO)5, a widely used precursor molecule for focused electron beam-induced deposition. In connection to recent experiments, the irradiation-induced fragmentation dynamics of an isolated Fe(CO)5+ molecule is studied and compared with that of Fe(CO)5+ embedded into an argon cluster. The appearance energies of different fragments of isolated Fe(CO)5+ agree with the recent experimental data. For Fe(CO)5+ embedded into an argon cluster, the simulations reproduce the experimentally observed suppression of Fe(CO)5+ fragmentation and provide an atomistic-level understanding of this effect. Understanding irradiation-driven fragmentation patterns for molecular systems in environments facilitates the advancement of atomistic models of irradiation-induced chemistry processes involving complex molecular systems.

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Linz U., Ed.; Ion Beam Therapy: Fundamentals, Technology, Clinical Applications; Springer: Berlin, 2012.

Schardt D.; Elsässer T.; Schulz-Ertner D. Heavy-ion tumor therapy: Physical and radiobiological benefits. Rev. Mod. Phys. 2010, 82, 383–425. 10.1103/RevModPhys.82.383. DOI

Solov’yov A. V., Ed.; Nanoscale Insights into Ion-Beam Cancer Therapy; Springer International Publishing: Cham, Switzerland, 2017.

Surdutovich E.; Solov’yov A. V. Multiscale approach to the physics of radiation damage with ions. Eur. Phys. J. D 2014, 68, 353.10.1140/epjd/e2014-50004-0. DOI

Nakano T.; Akamatsu K.; Tsuda M.; Tujimoto A.; Hirayama R.; Hiromoto T.; Tamada T.; Ide H.; Shikazono N. Formation of clustered DNA damage in vivo upon irradiation with ionizing radiation: Visualization and analysis with atomic force microscopy. Proc. Natl. Acad. Sci. U. S. A. 2022, 119, e2119132119.10.1073/pnas.2119132119. PubMed DOI PMC

Mifsud D. V.; Juhász Z.; Herczku P.; Kovács S. T. S.; Ioppolo S.; Kaňuchová Z.; Czentye M.; Hailey P. A.; Muiña A. T.; Mason N. J.; et al. Electron irradiation and thermal chemistry studies of interstellar and planetary ice analogues at the ICA astrochemistry facility. Eur. Phys. J. D 2021, 75, 182.10.1140/epjd/s10053-021-00192-7. DOI

Mifsud D. V.; Hailey P. A.; Herczku P.; Sulik B.; Juhász Z.; Kovács S. T. S.; Kaňuchová Z.; Ioppolo S.; McCullough R.; Paripás B.; et al. Comparative electron irradiations of amorphous and crystalline astrophysical ice analogues. Phys. Chem. Chem. Phys. 2022, 24, 10974–10984. 10.1039/D2CP00886F. PubMed DOI

Tielens A. G. G. M. The molecular universe. Rev. Mod. Phys. 2013, 85, 1021.10.1103/RevModPhys.85.1021. DOI

Utke I., Moshkalev S., Russell P., Eds.; Nanofabrication Using Focused Ion and Electron Beams; Oxford University Press: New York, 2012.

De Teresa J. M., Ed.; Nanofabrication: Nanolithography Techniques and Their Applications; IOP Publishing Ltd: Bristol, 2020.

Winkler R.; Fowlkes J. D.; Rack P. D.; Plank H. 3D nanoprinting via focused electron beams. J. Appl. Phys. 2019, 125, 210901.10.1063/1.5092372. DOI

Huth M.; Porrati F.; Barth S. Living up to its potential—Direct-write nanofabrication with focused electron beams. J. Appl. Phys. 2021, 130, 170901.10.1063/5.0064764. DOI

Thorman R. M.; Ragesh Kumar T. P.; Fairbrother D. H.; Ingólfsson O. The role of low-energy electrons in focused electron beam induced deposition: Four case studies of representative precursors. Beilstein J. Nanotechnol. 2015, 6, 1904–1926. 10.3762/bjnano.6.194. PubMed DOI PMC

Utke I.; Swiderek P.; Höflich K.; Madajska K.; Jurczyk J.; Martinović P.; Szymańska I. B. Coordination and organometallic precursors of group 10 and 11: Focused electron beam induced deposition of metals and insight gained from chemical vapour deposition, atomic layer deposition, and fundamental surface and gas phase studies. Coord. Chem. Rev. 2022, 458, 213851.10.1016/j.ccr.2021.213851. DOI

Prosvetov A.; Verkhovtsev A. V.; Sushko G.; Solov’yov A. V. Irradiation-driven molecular dynamics simulation of the FEBID process for Pt(PF3)4. Beilstein J. Nanotechnol. 2021, 12, 1151–1172. 10.3762/bjnano.12.86. PubMed DOI PMC

Prosvetov A.; Verkhovtsev A. V.; Sushko G.; Solov’yov A. V. Atomistic simulation of the FEBID-driven growth of iron-based nanostructures. Phys. Chem. Chem. Phys. 2022, 24, 10807–10819. 10.1039/D2CP00809B. PubMed DOI

Swiderek P.; Marbach H.; Hagen C. W. Chemistry for electron-induced nanofabrication. Beilstein J. Nanotechnol. 2018, 9, 1317–1320. 10.3762/bjnano.9.124. PubMed DOI PMC

Yu J.-C.; Abdel-Rahman M. K.; Fairbrother D. H.; McElwee-White L. Charged particle-induced surface reactions of organometallic complexes as a guide to precursor design for electron- and ion-induced deposition of nanostructures. ACS Appl. Mater. Interfaces 2021, 13, 48333–48348. 10.1021/acsami.1c12327. PubMed DOI

Barth S.; Huth M.; Jungwirth F. Precursors for direct-write nanofabrication with electrons. J. Mater. Chem. C 2020, 8, 15884–15919. 10.1039/D0TC03689G. DOI

Lacko M.; Papp P.; Wnorowski K.; Matejčík Š. Electron-induced ionization and dissociative ionization of iron pentacarbonyl molecules. Eur. Phys. J. D 2015, 69, 84.10.1140/epjd/e2015-50721-8. DOI

Allan M.; Lacko M.; Papp P.; Matejčík Š.; Zlatar M.; Fabrikant I. I.; Kočišek J.; Fedor J. Dissociative electron attachment and electronic excitation in Fe(CO)5. Phys. Chem. Chem. Phys. 2018, 20, 11692–11701. 10.1039/C8CP01387J. PubMed DOI

Ribar A.; Danko M.; Országh J.; Ferreira da Silva F.; Utke I.; Matejčík Š. Dissociative excitation study of iron pentacarbonyl molecule. Eur. Phys. J. D 2015, 69, 117.10.1140/epjd/e2015-60271-8. DOI

Lengyel J.; Kočišek J.; Fárník M.; Fedor J. Self-scavenging of electrons in Fe(CO)5 aggregates deposited on argon nanoparticles. J. Phys. Chem. C 2016, 120, 7397–7402. 10.1021/acs.jpcc.6b00901. DOI

Lengyel J.; Fedor J.; Fárník M. Ligand stabilization and charge transfer in dissociative ionization of Fe(CO)5 aggregates. J. Phys. Chem. C 2016, 120, 17810–17816. 10.1021/acs.jpcc.6b05852. DOI

Lengyel J.; Papp P.; Matejčík Š.; Kočišek J.; Fárník M.; Fedor J. Suppression of low-energy dissociative electron attachment in Fe(CO)5 upon clustering. Beilstein J. Nanotechnol. 2017, 8, 2200–2207. 10.3762/bjnano.8.219. PubMed DOI PMC

Lengyel J.; Pysanenko A.; Swiderek P.; Heiz U.; Fárník M.; Fedor J. Water-assisted electron-induced chemistry of the nanofabrication precursor iron pentacarbonyl. J. Phys. Chem. A 2021, 125, 1919–1926. 10.1021/acs.jpca.1c00135. PubMed DOI

Massey S.; Bass A. D.; Sanche L. Role of low-energy electrons (< 35 eV) in the degradation of Fe(CO)5 for focused electron beam induced deposition applications: Study by electron stimulated desorption of negative and positive ions. J. Phys. Chem. C 2015, 119, 12708–12719. 10.1021/acs.jpcc.5b02684. DOI

Bilgilisoy E.; Thorman R. M.; Barclay M. S.; Marbach H.; Fairbrother D. H. Low energy electron- and ion-induced surface reactions of Fe(CO)5 thin films. J. Phys. Chem. C 2021, 125, 17749–17760. 10.1021/acs.jpcc.1c05826. DOI

Cai Z.; Chen S.; Wang L.-W. Dissociation path competition of radiolysis ionization-induced molecule damage under electron beam illumination. Chem. Sci. 2019, 10, 10706–10715. 10.1039/C9SC04100A. PubMed DOI PMC

Wang Z.; Xu X.; Zhang F.; Qian C. TDDFT investigation of excitation of water tetramer under femtosecond laser pulse irradiation. Int. J. Mod. Phys. B 2018, 32, 1850113.10.1142/S0217979218501138. DOI

Hervé du Penhoat M.-A.; Hamila A.; Gaigeot M.-P.; Vuilleumier R.; Fujii K.; Yokoya A.; Politis M.-F. Ab initio molecular dynamics simulations to interpret the molecular fragmentation induced in deoxyribose by synchrotron soft X-rays. Quantum Beam Sci. 2019, 3, 24.10.3390/qubs3040024. DOI

Sushko G. B.; Solov’yov I. A.; Verkhovtsev A. V.; Volkov S. N.; Solov’yov A. V. Studying chemical reactions in biological systems with MBN Explorer: Implementation of molecular mechanics with dynamical topology. Eur. Phys. J. D 2016, 70, 12.10.1140/epjd/e2015-60424-9. DOI

Sushko G. B.; Solov’yov I. A.; Solov’yov A. V. Molecular dynamics for irradiation driven chemistry: application to the FEBID process. Eur. Phys. J. D 2016, 70, 217.10.1140/epjd/e2016-70283-5. DOI

Solov’yov I. A.; Yakubovich A. V.; Nikolaev P. V.; Volkovets I.; Solov’yov A. V. MesoBioNano Explorer – A universal program for multiscale computer simulations of complex molecular structure and dynamics. J. Comput. Chem. 2012, 33, 2412–2439. 10.1002/jcc.23086. PubMed DOI

Solov’yov I. A.; Korol A. V.; Solov’yov A. V.. Multiscale Modeling of Complex Molecular Structure and Dynamics with MBN Explorer; Springer International Publishing: Cham, Switzerland, 2017.

de Vera P.; Azzolini M.; Sushko G.; Abril I.; Garcia-Molina R.; Dapor M.; Solov’yov I. A.; Solov’yov A. V. Multiscale simulation of the focused electron beam induced deposition process. Sci. Rep. 2020, 10, 20827.10.1038/s41598-020-77120-z. PubMed DOI PMC

Solov’yov I. A., Verkhovtsev A. V., Korol A. V., Solov’yov A. V., Eds.; Dynamics of Systems on the Nanoscale; Springer International Publishing: Cham, Switzerland, 2022.

Lukasczyk T.; Schirmer M.; Steinrück H.-P.; Marbach H. Electron-beam-induced deposition in ultrahigh vacuum: lithographic fabrication of clean iron nanostructures. Small 2008, 4, 841–846. 10.1002/smll.200701095. PubMed DOI

Gavagnin M.; Wanzenboeck H. D.; Belić D.; Bertagnolli E. Synthesis of individually tuned nanomagnets for Nanomagnet Logic by direct write focused electron beam induced deposition. ACS Nano 2013, 7, 777–784. 10.1021/nn305079a. PubMed DOI

Gavagnin M.; Wanzenboeck H. D.; Belic D.; Shawrav M. M.; Persson A.; Gunnarsson K.; Svedlindh P.; Bertagnolli E. Magnetic force microscopy study of shape engineered FEBID iron nanostructures. Phys. Status Solidi A 2014, 211, 368–374. 10.1002/pssa.201330114. DOI

De Teresa J. M.; Fernández-Pacheco A.; Córdoba R.; Serrano-Ramón L.; Sangiao S.; Ibarra M. R. Review of magnetic nanostructures grown by focused electron beam induced deposition (FEBID). J. Phys. D: Appl. Phys. 2016, 49, 243003.10.1088/0022-3727/49/24/243003. DOI

Sushko G. B.; Solov’yov I. A.; Solov’yov A. V. Modeling MesoBioNano systems with MBN Studio made easy. J. Mol. Graph. Model. 2019, 88, 247–260. 10.1016/j.jmgm.2019.02.003. PubMed DOI

Li C.; Chin C. H.; Zhu T.; Zhang J. Z. H. An ab initio/RRKM study of the reaction mechanism and product branching ratios of CH3OH+ and CH3OH+2 dissociation. J. Mol. Struct. 2020, 1217, 128410.10.1016/j.molstruc.2020.128410. DOI

Graves V.; Cooper B.; Tennyson J. Calculated electron impact ionisation fragmentation patterns. J. Phys. B: At. Mol. Opt. Phys. 2021, 54, 235203.10.1088/1361-6455/ac42db. DOI

Ranković M.; Chalabala J.; Zawadzki M.; Kočišek J.; Slavíček P.; Fedor J. Dissociative ionization dynamics of dielectric gas C3F7CN. Phys. Chem. Chem. Phys. 2019, 21, 16451–16458. 10.1039/C9CP02188D. PubMed DOI

Verkhovtsev A.; Korol A. V.; Solovyov A. V. Classical molecular dynamics simulations of fusion and fragmentation in fullerene-fullerene collisions. Eur. Phys. J. D 2017, 71, 212.10.1140/epjd/e2017-80117-7. DOI

de Vera P.; Verkhovtsev A.; Sushko G.; Solov’yov A. V. Reactive molecular dynamics simulations of organometallic compound W(CO)6 fragmentation. Eur. Phys. J. D 2019, 73, 215.10.1140/epjd/e2019-100232-9. DOI

Friis I.; Verkhovtsev A.; Solov’yov I. A.; Solov’yov A. V. Modeling the effect of ion-induced shock waves and DNA breakage with the reactive CHARMM force field. J. Comput. Chem. 2020, 41, 2429–2439. 10.1002/jcc.26399. PubMed DOI

Friis I.; Verkhovtsev A. V.; Solov’yov I. A.; Solov’yov A. V. Lethal DNA damage caused by ion-induced shock waves in cells. Phys. Rev. E 2021, 104, 054408.10.1103/PhysRevE.104.054408. PubMed DOI

Verkhovtsev A. V.; Solov’yov I. A.; Solov’yov A. V. Irradiation-driven molecular dynamics: a review. Eur. Phys. J. D 2021, 75, 213.10.1140/epjd/s10053-021-00223-3. DOI

Portius P.; Bühl M.; George M. W.; Grevels F.-W.; Turner J. J. Structure and dynamics of iron pentacarbonyl. Organometallics 2019, 38, 4288–4297. 10.1021/acs.organomet.9b00559. DOI

Ricca A.; Bauschlicher C. W. Jr. Successive binding energies of Fe(CO)5+. J. Phys. Chem. 1994, 98, 12899–12903. 10.1021/j100100a015. DOI

Rall J. M.; Schorpp M.; Keilwerth M.; Mayländer M.; Friedmann C.; Daub M.; Richert S.; Meyer K.; Krossing I. Synthesis and characterization of stable iron pentacarbonyl radical cation salts. Angew. Chem., Int. Ed. 2022, 61, e202204080.10.1002/anie.202283261. PubMed DOI PMC

Frisch M. J.; Trucks G. W.; Schlegel H. B.; Scuseria G. E.; Robb M. A.; Cheeseman J. R.; Scalmani G.; Barone V.; Petersson G. A.; Nakatsuji H.; et al.Gaussian Inc 16, Revision C.01; Gaussian Inc.: Wallingford, CT, 2016.

The NIST Chemistry WebBook. https://webbook.nist.gov/ (accessed: 2023-01-03).

Mayo S. L.; Olafson B. D.; Goddard W. A. DREIDING: A generic force field for molecular simulations. J. Phys. Chem. 1990, 94, 8897–8909. 10.1021/j100389a010. DOI

Talu O.; Myers A. L. Reference potentials for adsorption of helium, argon, methane, and krypton in high-silica zeolites. Colloids Surf. A: Physicochem. Eng. Asp. 2001, 187–188, 83–93. 10.1016/S0927-7757(01)00628-8. DOI

Gerchikov L. G.; Ipatov A. N.; Solov’yov A. V.; Greiner W. Non-adiabatic electron-ion coupling in dynamical jellium model for metal clusters. J. Phys. B: At. Mol. Opt. Phys. 2000, 33, 4905–4926. 10.1088/0953-4075/33/21/330. DOI

Coplan M. A.; Moore J. H.; Doering J. P. (e, 2e) spectroscopy. Rev. Mod. Phys. 1994, 66, 985.10.1103/RevModPhys.66.985. DOI

Fedor J.; Poterya V.; Pysanenko A.; Fárník M. Cluster cross sections from pickup measurements: Are the established methods consistent?. J. Chem. Phys. 2011, 135, 104305.10.1063/1.3633474. PubMed DOI

Lengyel J.; Kočišek J.; Poterya V.; Pysanenko A.; Svrčková P.; Fárník M.; Zaouris D.; Fedor J. Uptake of atmospheric molecules by ice nanoparticles: Pickup cross sections. J. Chem. Phys. 2012, 137, 034304.10.1063/1.4733987. PubMed DOI

Pysanenko A.; Habartová A.; Svrčková P.; Lengyel J.; Poterya V.; Roeselová M.; Fedor J.; Fárník M. Lack of aggregation of molecules on ice nanoparticles. J. Phys. Chem. A 2015, 119, 8991–8999. 10.1021/acs.jpca.5b05368. PubMed DOI

Fárník M.; Fedor J.; Kočišek J.; Lengyel J.; Pluhařová E.; Poterya V.; Pysanenko A. Pickup and reactions of molecules on clusters relevant for atmospheric and interstellar processes. Phys. Chem. Chem. Phys. 2021, 23, 3195–3213. 10.1039/D0CP06127A. PubMed DOI

Jacox M. E. The spectroscopy of molecular reaction intermediates trapped in the solid rare gases. Chem. Soc. Rev. 2002, 31, 108–115. 10.1039/b102907j. PubMed DOI

Fedor J.; Kočišek J.; Poterya V.; Votava O.; Pysanenko A.; Lipciuc L.; Kitsopoulos T. N.; Fárník M. Velocity map imaging of HBr photodissociation in large rare gas clusters. J. Chem. Phys. 2011, 134, 154303.10.1063/1.3578610. PubMed DOI

Chachereau A.; Fedor J.; Janečková R.; Kočišek J.; Rabie M.; Franck C. M. Electron attachment properties of c-C4F8O in different environments. J. Phys. D: Appl. Phys. 2016, 49, 375201.10.1088/0022-3727/49/37/375201. DOI

Kočišek J.; Sedmidubská B.; Indrajith S.; Fárník M.; Fedor J. Electron Attachment to Microhydrated Deoxycytidine Monophosphate. J. Phys. Chem. B 2018, 122, 5212–5217. 10.1021/acs.jpcb.8b03033. PubMed DOI

Fabrikant I. I. Electron attachment to molecules in a cluster environment: suppression and enhancement effects. Eur. Phys. J. D 2018, 72, 96.10.1140/epjd/e2018-90082-2. PubMed DOI

Zlatar M.; Allan M.; Fedor J. Excited states of Pt(PF3)4 and their role in focused electron beam induced deposition. J. Phys. Chem. C 2016, 120, 10667–10674. 10.1021/acs.jpcc.6b02660. DOI

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