“Development of a ReaxFF reactive force field for intrinsic point defects in titanium dioxide”. Huygh S, Bogaerts A, van Duin ACT, Neyts EC, Computational materials science 95, 579 (2014). http://doi.org/10.1016/j.commatsci.2014.07.056
Abstract: A reactive ReaxFF force field is developed for studying the influence of intrinsic point defects on the chemistry with TiO2 condensed phases. The force field parameters are optimized to ab initio data for the equations of state, relative phase stabilities for titanium and titanium dioxide, potential energy differences for (TiO2)n-clusters (n = 116). Also data for intrinsic point defects in anatase were added. These data contain formation energies for interstitial titanium and oxygen vacancies, diffusion barriers of the oxygen vacancies and molecular oxygen adsorption on a reduced anatase (101) surface. Employing the resulting force field, we study the influence of concentration of oxygen vacancies and expansion or compression of an anatase surface on the diffusion of the oxygen vacancies. Also the barrier for oxygen diffusion in the subsurface region is evaluated using this force field. This diffusion barrier of 27.7 kcal/mol indicates that the lateral redistribution of oxygen vacancies on the surface and in the subsurface will be dominated by their diffusion in the subsurface, since both this barrier as well as the barriers for diffusion from the surface to the subsurface and vice versa (17.07 kcal/mol and 21.91 kcal/mol, respectively, as calculated with DFT), are significantly lower than for diffusion on the surface (61.12 kcal/mol as calculated with DFT).
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.292
Times cited: 15
DOI: 10.1016/j.commatsci.2014.07.056
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“Formation of endohedral Ni@C60 and exohedral NiC60 metallofullerene complexes by simulated ion implantation”. Neyts EC, Bogaerts A, Carbon 47, 1028 (2009). http://doi.org/10.1016/j.carbon.2008.12.023
Abstract: The interaction of thermal and hyperthermal Ni ions with gas-phase C60 fullerene was investigated at two temperatures with classical molecular dynamics simulations using a recently developed interatomic many-body potential. The interaction between Ni and C60 is characterized in terms of the NiC60 binding sites, complex formation, and the collision and temperature induced deformation of the C60 cage structure. The simulations show how ion implantation theoretically allows the synthesis of both endohedral Ni@C60 and exohedral NiC60 metallofullerene complexes.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.337
Times cited: 15
DOI: 10.1016/j.carbon.2008.12.023
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“Nanoscale thermodynamic aspects of plasma catalysis”. Neyts EC, Ostrikov K(K), Catalysis today 256, 23 (2015). http://doi.org/10.1016/j.cattod.2015.02.025
Abstract: Plasma catalysis continues to gain increasing scientific interest, both in established fields like toxic waste abatement and emerging fields like greenhouse gas conversion into value-added chemicals. Attention is typically focused on the obtained conversion process selectivity, rates and energy efficiency. Much less attention is usually paid to the underlying mechanistic aspects of the processes that occur. In this contribution, we critically examine a number of fundamentally important nanoscale thermodynamic aspects of plasma catalysis, which are very relevant to these processes but so far have been overlooked or insufficiently covered in the plasma catalysis literature.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.636
Times cited: 14
DOI: 10.1016/j.cattod.2015.02.025
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“On the low-temperature growth mechanism of single walled carbon nanotubes in plasma enhanced chemical vapor deposition”. Shariat M, Shokri B, Neyts EC, Chemical physics letters 590, 131 (2013). http://doi.org/10.1016/j.cplett.2013.10.061
Abstract: Despite significant progress in single walled carbon nanotube (SWCNT) production by plasma enhanced chemical vapor deposition (PECVD), the growth mechanism in this method is not clearly understood. We employ reactive molecular dynamics simulations to investigate how plasma-based deposition allows growth at low temperature. We first investigate the SWCNT growth mechanism at low and high temperatures under conditions similar to thermal CVD and PECVD. We then show how ion bombardment during the nucleation stage increases the carbon solubility in the catalyst at low temperature. Finally, we demonstrate how moderate energy ions sputter amorphous carbon allowing for SWCNT growth at 500 K. (C) 2013 Elsevier B. V. All rights reserved.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 1.815
Times cited: 14
DOI: 10.1016/j.cplett.2013.10.061
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“Adsorption of C and CHx radicals on anatase (001) and the influence of oxygen vacancies”. Huygh S, Neyts EC, The journal of physical chemistry: C : nanomaterials and interfaces 119, 4908 (2015). http://doi.org/10.1021/jp5127249
Abstract: The adsorption of C and CHx radicals on anatase (001) was studied using DFT within the generalized gradient approximation using the Perde-Burke-Ernzerhof (PBE) functional. We have studied the influence of oxygen vacancies in and at the surface on the adsorption properties of the radicals. For the oxygen vacancies in anatase (001), the most stable vacancy is located at the surface. For this vacancy, the maximal adsorption strength of C and CH decreases compared to the adsorption on the stoichiometric surface, but it increases for CH2 and CH3. If an oxygen vacancy is present in the first subsurface layer, the maximal adsorption strength increases for C, CH, CH2, and CH3. When the vacancy is present in the next subsurface layer, we find that only the CH3 adsorption is enhanced, while the maximal adsorption energies for the other radical species decrease. Not only does the precise location of the oxygen vacancy determine the maximal adsorption interaction, it also influences the adsorption strengths of the radicals at different surface configurations. This determines the probability of finding a certain adsorption configuration at the surface, which in turn influences the possible surface reactions. We find that C preferentially adsorbs far away from the oxygen vacancy, while CH2 and CH3 adsorb preferentially at the oxygen vacancy site. A fraction of CH partially adsorbs at the oxygen vacancy, and another fraction adsorbs further away from the vacancy.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
Times cited: 13
DOI: 10.1021/jp5127249
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“Understanding polyethylene surface functionalization by an atmospheric He/O2 plasma through combined experiments and simulations”. Dufour T, Minnebo J, Abou Rich S, Neyts EC, Bogaerts A, Reniers F, Journal of physics: D: applied physics 47, 224007 (2014). http://doi.org/10.1088/0022-3727/47/22/224007
Abstract: High density polyethylene surfaces were exposed to the atmospheric post-discharge of a radiofrequency plasma torch supplied in helium and oxygen. Dynamic water contact angle measurements were performed to evaluate changes in surface hydrophilicity and angle resolved x-ray photoelectron spectroscopy was carried out to identify the functional groups responsible for wettability changes and to study their subsurface depth profiles, up to 9 nm in depth. The reactions leading to the formation of CO, C = O and OC = O groups were simulated by molecular dynamics. These simulations demonstrate that impinging oxygen atoms do not react immediately upon impact but rather remain at or close to the surface before eventually reacting. The simulations also explain the release of gaseous species in the ambient environment as well as the ejection of low molecular weight oxidized materials from the surface.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.588
Times cited: 13
DOI: 10.1088/0022-3727/47/22/224007
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“Two-dimensional WS2 nanoribbon deposition by conversion of pre-patterned amorphous silicon”. Heyne MH, de Marneffe J-F, Delabie A, Caymax M, Neyts EC, Radu I, Huyghebaert C, De Gendt S, Nanotechnology 28, 04LT01 (2017). http://doi.org/10.1088/1361-6528/AA510C
Abstract: We present a method for area selective deposition of 2D WS2 nanoribbons with tunable thickness on a dielectric substrate. The process is based on a complete conversion of a prepatterned, H-terminated Si layer to metallic W by WF6, followed by in situ sulfidation by H2S. The reaction process, performed at 450 degrees C, yields nanoribbons with lateral dimension down to 20 nm and with random basal plane orientation. The thickness of the nanoribbons is accurately controlled by the thickness of the pre-deposited Si layer. Upon rapid thermal annealing at 900 degrees C under inert gas, the WS2 basal planes align parallel to the substrate.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.44
Times cited: 13
DOI: 10.1088/1361-6528/AA510C
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“Molecular Dynamics Simulations for Plasma-Surface Interactions: Molecular Dynamics Simulations…”. Neyts EC, Brault P, Plasma processes and polymers 14, 1600145 (2017). http://doi.org/10.1002/ppap.201600145
Abstract: Plasma-surface interactions are in general highly complex due to the interplay of many concurrent processes. Molecular dynamics simulations provide insight in some of these processes, subject to the accessible time and length scales, and the availability of suitable force fields. In this introductory tutorial-style review, we aim to describe the current capabilities and limitations of molecular dynamics simulations in this field, restricting ourselves to low-temperature nonthermal plasmas. Attention is paid to the simulation of the various fundamental processes occurring, including sputtering, etching, implantation, and deposition, as well as to what extent the basic plasma components can be accounted for, including ground state and excited species, electric fields, ions, photons, and electrons. A number of examples is provided, giving an bird’s eye overview of the current state of the field.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.846
Times cited: 13
DOI: 10.1002/ppap.201600145
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“Fluorinesilicon surface reactions during cryogenic and near room temperature etching”. Tinck S, Neyts EC, Bogaerts A, The journal of physical chemistry: C : nanomaterials and interfaces 118, 30315 (2014). http://doi.org/10.1021/jp5108872
Abstract: Cyrogenic etching of silicon is envisaged to enable better control over plasma processing in the microelectronics industry, albeit little is known about the fundamental differences compared to the room temperature process. We here present molecular dynamics simulations carried out to obtain sticking probabilities, thermal desorption rates, surface diffusion speeds, and sputter yields of F, F2, Si, SiF, SiF2, SiF3, SiF4, and the corresponding ions on Si(100) and on SiF13 surfaces, both at cryogenic and near room temperature. The different surface behavior during conventional etching and cryoetching is discussed. F2 is found to be relatively reactive compared to other species like SiF03. Thermal desorption occurs at a significantly lower rate under cryogenic conditions, which results in an accumulation of physisorbed species. Moreover, ion incorporation is often observed for ions with energies of 30400 eV, which results in a relatively low net sputter yield. The obtained results suggest that the actual etching of Si, under both cryogenic and near room temperature conditions, is based on the complete conversion of the Si surface to physisorbed SiF4, followed by subsequent sputtering of these molecules, instead of direct sputtering of the SiF03 surface.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
Times cited: 11
DOI: 10.1021/jp5108872
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“Multi-level molecular modelling for plasma medicine”. Bogaerts A, Khosravian N, Van der Paal J, Verlackt CCW, Yusupov M, Kamaraj B, Neyts EC, Journal of physics: D: applied physics 49, 054002 (2016). http://doi.org/10.1088/0022-3727/49/5/054002
Abstract: Modelling at the molecular or atomic scale can be very useful for obtaining a better insight in plasma medicine. This paper gives an overview of different atomic/molecular scale modelling approaches that can be used to study the direct interaction of plasma species with biomolecules or the consequences of these interactions for the biomolecules on a somewhat longer time-scale. These approaches include density functional theory (DFT), density functional based tight binding (DFTB), classical reactive and non-reactive molecular dynamics (MD) and united-atom or coarse-grained MD, as well as hybrid quantum mechanics/molecular mechanics (QM/MM) methods. Specific examples will be given for three important types of biomolecules, present in human cells, i.e. proteins, DNA and phospholipids found in the cell membrane. The results show that each of these modelling approaches has its specific strengths and limitations, and is particularly useful for certain applications. A multi-level approach is therefore most suitable for obtaining a global picture of the plasma–biomolecule interactions.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.588
Times cited: 11
DOI: 10.1088/0022-3727/49/5/054002
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“Atomic scale behavior of oxygen-based radicals in water”. Verlackt CCW, Neyts EC, Bogaerts A, Journal of physics: D: applied physics 50, 11LT01 (2017). http://doi.org/10.1088/1361-6463/aa5c60
Abstract: Cold atmospheric pressure plasmas in and in contact with liquids represent a growing field of research for various applications. Understanding the interactions between the plasma generated species and the liquid is crucial. In this work we perform molecular dynamics (MD) simulations based on a quantum mechanical method, i.e. density-functional based tight-binding (DFTB), to examine the interactions of OH radicals and O atoms in bulk water. Our calculations reveal that the transport of OH radicals through water is not only governed by diffusion, but also by an equilibrium reaction of H-abstraction with water molecules. Furthermore, when two OH radicals encounter each other, they either form a stable cluster, or react, resulting in the formation of a new water molecule and an O atom. In addition,
the O atoms form either oxywater (when in singlet configuration) or they remain stable in solution (when in triplet configuration), stressing the important role that O atoms can play in aqueous solution, and in contact with biomolecules. Our observations are in line with both experimental and ab initio results from the literature.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.588
Times cited: 11
DOI: 10.1088/1361-6463/aa5c60
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“Enhancement of plasma generation in catalyst pores with different shapes”. Zhang Y-R, Neyts EC, Bogaerts A, Plasma sources science and technology 27, 055008 (2018). http://doi.org/10.1088/1361-6595/aac0e4
Abstract: Plasma generation inside catalyst pores is of utmost importance for plasma catalysis, as the existence of plasma species inside the pores affects the active surface area of the catalyst available to the plasma species for catalytic reactions. In this paper, the electric field enhancement, and thus the plasma production inside catalyst pores with different pore shapes is studied with a two-dimensional fluid model. The results indicate that the electric field will be significantly enhanced near tip-like structures. In a conical pore with small opening, the strongest electric field appears at the opening and bottom corners of the pore, giving rise to a prominent ionization rate throughout the pore. For a cylindrical pore, the electric field is only enhanced at the bottom corners of the pore, with lower absolute value, and thus the ionization rate inside the pore is only slightly enhanced. Finally, in a conical pore with large opening, the electric field is characterized by a maximum at the bottom of the pore, yielding a similar behavior for the ionization rate. These results demonstrate that the shape of the pore has a significantly influence on the electric field enhancement, and thus modifies the plasma properties.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.302
Times cited: 11
DOI: 10.1088/1361-6595/aac0e4
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“How do plasma-generated OH radicals react with biofilm components? Insights from atomic scale simulations”. Khosravian N, Bogaerts A, Huygh S, Yusupov M, Neyts EC, Biointerphases 10, 029501 (2015). http://doi.org/10.1116/1.4904339
Abstract: The application of nonthermal atmospheric pressure plasma is emerging as an alternative and efficient technique for the inactivation of bacterial biofilms. In this study, reactive molecular dynamics simulations were used to examine the reaction mechanisms of hydroxyl radicals, as key reactive oxygen plasma species in biological systems, with several organic molecules (i.e., alkane, alcohol, carboxylic acid, and amine), as prototypical components of biomolecules in the biofilm. Our results demonstrate that organic molecules containing hydroxyl and carboxyl groups may act as trapping agents for the OH radicals. Moreover, the impact of OH radicals on N-acetyl-glucosamine, as constituent component of staphylococcus epidermidis biofilms, was investigated. The results show how impacts of OH radicals lead to hydrogen abstraction and subsequent molecular damage. This study thus provides new data on the reaction mechanisms of plasma species, and particularly the OH radicals, with fundamental components of bacterial biofilms.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.603
Times cited: 10
DOI: 10.1116/1.4904339
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“A DFT study of H-dissolution into the bulk of a crystalline Ni(111) surface: a chemical identifier for the reaction kinetics”. Shirazi M, Bogaerts A, Neyts EC, Physical chemistry, chemical physics 19, 19150 (2017). http://doi.org/10.1039/C7CP03662K
Abstract: In this study, we investigated the diffusion of H-atoms to the subsurface and their further diffusion into the bulk of a Ni(111) crystal by means of density functional theory calculations in the context of thermal and plasma-assisted catalysis. The H-atoms at the surface can originate from the dissociative adsorption of H2 or CH4 molecules, determining the surface H-coverage. When a threshold H-coverage is passed, corresponding to 1.00 ML for the crystalline Ni(111) surface, the surface-bound H-atoms start to diffuse to the subsurface. A similar threshold coverage is observed for the interstitial H-coverage. Once the interstitial sites are filled up with a coverage above 1.00 ML of H, dissolution of interstitial H-atoms to the layer below the interstitial sites will be initiated. Hence, by applying a high pressure or inducing a reactive plasma and high temperature, increasing the H-flux to the surface, a large amount of hydrogen can diffuse in a crystalline metal like Ni and can be absorbed. The formation of metal hydride may modify the entire reaction kinetics of the system. Equivalently, the H-atoms in the bulk can easily go back to the surface and release a large amount of heat. In a plasma process, H-atoms are formed in the plasma, and therefore the energy barrier for dissociative adsorption is dismissed, thus allowing achievement of the threshold coverage without applying a high pressure as in a thermal process. As a result, depending on the crystal plane and type of metal, a large number of H-atoms can be dissolved (absorbed) in the metal catalyst, explaining the high efficiency of plasma-assisted catalytic reactions. Here, the mechanism of H-dissolution is established as a chemical identifier for the investigation of the reaction kinetics of a chemical process.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.123
Times cited: 10
DOI: 10.1039/C7CP03662K
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“Phosphatidylserine flip-flop induced by oxidation of the plasma membrane: a better insight by atomic scale modeling”. Razzokov J, Yusupov M, Vanuytsel S, Neyts EC, Bogaerts A, Plasma processes and polymers 14, 1700013 (2017). http://doi.org/10.1002/ppap.201700013
Abstract: We perform molecular dynamics simulations to study the flip-flop motion of phosphatidylserine (PS) across the plasma membrane upon increasing oxidation degree of the membrane. Our computational results show that an increase of the oxidation degree in the lipids leads to a decrease of the free energy barrier for translocation of PS through the membrane. In other words, oxidation of the lipids facilitates PS flip-flop motion across the membrane, because in native phospholipid bilayers this is only a “rare event” due to the high energy barriers for the translocation of PS. The present study provides an atomic-scale insight into the mechanisms of the PS flip-flop upon oxidation of lipids, as produced for example by cold atmospheric plasma, in living cells.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.846
Times cited: 9
DOI: 10.1002/ppap.201700013
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“Arresting aqueous swelling of layered graphene-oxide membranes with H3O+ and OH- ions”. Gogoi A, Neyts EC, Milošević, MV, Peeters FM, ACS applied materials and interfaces 14, 34946 (2022). http://doi.org/10.1021/ACSAMI.2C05926
Abstract: Over the past decade, graphene oxide (GO) has emerged as a promising membrane material with superior separation performance and intriguing mechanical/chemical stability. However, its practical implementation remains very challenging primarily because of its undesirable swelling in an aqueous environment. Here, we demonstrated that dissociation of water molecules into H3O+ and OH- ions inside the interlayer gallery of a layered GO membrane can strongly affect its stability and performance. We reveal that H3O+ and OH- ions form clusters inside the GO laminates that impede the permeance of water and salt ions through the membrane. Dynamics of those clusters is sensitive to an external ac electric field, which can be used to tailor the membrane performance. The presence of H3O+ and OH- ions also leads to increased stability of the hydrogen bond (H-bond) network among the water molecules and the GO layers, which further reduces water permeance through the membrane, while crucially imparting stability to the layered GO membrane against undesirable swelling. KEYWORDS: layered graphene-oxide membrane, aqueous stability, H3O+ and OH- ions, external electric field, molecular dynamics
Keywords: A1 Journal article; Engineering sciences. Technology; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 9.5
Times cited: 9
DOI: 10.1021/ACSAMI.2C05926
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“The role of ions in plasma catalytic carbon nanotube growth : a review”. Neyts EC, Frontiers of Chemical Science and Engineering 9, 154 (2015). http://doi.org/10.1007/s11705-015-1515-5
Abstract: While it is well-known that the plasma-enhanced catalytic chemical vapor deposition (PECVD) of carbon nanotubes (CNTs) offers a number of advantages over thermal CVD, the influence of the various individual contributing factors is not well understood. Especially the role of ions is unclear, since ions in plasmas are generally associated with sputtering rather than with growing a material. Even so, various studies have demonstrated the beneficial effects of ion bombardment during the growth of CNTs. This review looks at the role of the ions in plasma-enhanced CNT growth as deduced from both experimental and simulation studies. Specific attention is paid to the beneficial effects of ion bombardment. Based on the available literature, it can be concluded that ions can be either beneficial or detrimental for carbon nanotube growth, depending on the exact conditions and the control over the growth process.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 1.712
Times cited: 8
DOI: 10.1007/s11705-015-1515-5
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“Modelling molecular adsorption on charged or polarized surfaces: a critical flaw in common approaches”. Bal KM, Neyts EC, Physical chemistry, chemical physics 20, 8456 (2018). http://doi.org/10.1039/C7CP08209F
Abstract: A number of recent computational material design studies based on density functional theory (DFT) calculations have put forward a new class of materials with electrically switchable chemical characteristics that can be exploited in the development of tunable gas storage and electrocatalytic applications. We find systematic flaws in almost every computational study of gas adsorption on polarized or charged surfaces, stemming from an improper and unreproducible treatment of periodicity, leading to very large errors of up to 3 eV in some cases. Two simple corrective procedures that lead to consistent results are proposed, constituting a crucial course correction to the research in the field.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.123
Times cited: 8
DOI: 10.1039/C7CP08209F
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“A comparative DFT study on CO oxidation reaction over Si-doped BC2N nanosheet and nanotube”. Nematollahi P, Neyts EC, Applied surface science 439, 934 (2018). http://doi.org/10.1016/J.APSUSC.2017.12.254
Abstract: In this study, we performed density functional theory (DFT) calculations to investigate different reaction mechanisms of CO oxidation catalyzed by the Si atom embedded defective BC2N nanostructures as well as the analysis of the structural and electronic properties. The structures of all the complexes are optimized and characterized by frequency calculations at the M062X/6-31G* computational level. Also, The electronic structures and thermodynamic parameters of adsorbed CO and O-2 molecules over Si-doped BC2N nanostructures are examined in detail. Moreover, to investigate the curvature effect on the CO oxidation reaction, all the adsorption and CO oxidation reactions on a finite-sized armchair (6,6) Si-BC2NNT are also studied. Our results indicate that there can be two possible pathways for the CO oxidation with O-2 molecule: O-2(g) + CO(g) -> O-2(ads) + CO(ads) -> CO2(g) + O-(ads) and O-(ads) + CO(g) -> CO2(g). The first reaction proceeds via the Langmuir-Hinshelwood (LH) mechanism while the second goes through the Eley-Rideal (ER) mechanism. On the other hand, by increasing the tube diameter, the energy barrier increases due to the strong adsorption energy of the O-2 molecule which is related to its dissociation over the tube surface. Our calculations indicate that the two step energy barrier of the oxidation reaction over Si-BC2NNS is less than that over the Si-BC2NNT. Hence, Si-BC2NNS may serve as an efficient and highly activated substrate to CO oxidation rather than (4,4) Si-BC2NNT. (C) 2018 Elsevier B.V. All rights reserved.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.387
Times cited: 8
DOI: 10.1016/J.APSUSC.2017.12.254
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“Ion irradiation for improved graphene network formation in carbon nanotube growth”. Neyts EC, Bogaerts A, Carbon 77, 790 (2014). http://doi.org/10.1016/j.carbon.2014.05.083
Abstract: Ion irradiation of carbon nanotubes very often leads to defect formation. However, we have recently shown that Ar ion irradiation in a limited energy window of 1025 eV may enhance the initial cap nucleation process, when the carbon network is in contact with the metal nanocatalyst. Here, we employ reactive molecular dynamics simulations to demonstrate that ion irradiation in a higher energy window of 1035 eV may also heal network defects after the nucleation stage through a non-metal-mediated mechanism, when the carbon network is no longer in contact with the metal nanocatalyst. The results demonstrate the possibility of beneficially utilizing ions in e.g. plasma-enhanced chemical vapour deposition of carbon nanotubes.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.337
Times cited: 7
DOI: 10.1016/j.carbon.2014.05.083
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“Structural modification of P-glycoprotein induced by OH radicals: Insights from atomistic simulations”. Khosravian N, Kamaraj B, Neyts EC, Bogaerts A, Scientific reports 6, 19466 (2016). http://doi.org/10.1038/srep19466
Abstract: This study reports on the possible effects of OH radical impact on the transmembrane domain 6 of P-glycoprotein, TM6, which plays a crucial role in drug binding in human cells. For the first time, we employ molecular dynamics (MD) simulations based on the self-consistent charge density functional tight binding (SCC-DFTB) method to elucidate the potential sites of fragmentation and mutation in this domain upon impact of OH radicals, and to obtain fundamental information about the underlying reaction mechanisms. Furthermore, we apply non-reactive MD simulations to investigate the long-term effect of this mutation, with possible implications for drug binding. Our simulations indicate that the interaction of OH radicals with TM6 might lead to the breaking of C-C and C-N peptide bonds, which eventually cause fragmentation of TM6. Moreover, according to our simulations, the OH radicals can yield mutation in the aromatic ring of phenylalanine in TM6, which in turn affects its structure. As TM6 plays an important role in the binding of a range of cytotoxic drugs with P-glycoprotein, any changes in its structure are likely to affect the response of the tumor cell in chemotherapy. This is crucial for cancer therapies based on reactive oxygen species, such as plasma treatment.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.259
Times cited: 7
DOI: 10.1038/srep19466
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“van der Waals density functionals applied to corundum-type sesquioxides : bulk properties and adsorption of CH3 and C6H6 on (0001) surfaces”. Dabaghmanesh S, Neyts EC, Partoens B, Physical chemistry, chemical physics 18, 23139 (2016). http://doi.org/10.1039/c6cp00346j
Abstract: van der Waals (vdW) forces play an important role in the adsorption of molecules on the surface of solids. However, the choice of the most suitable vdW functional for different systems is an essential problem which must be addressed for different systems. The lack of a systematic study on the performance of the vdW functionals in the bulk and adsorption properties of metal-oxides motivated us to examine different vdW approaches and compute the bulk and molecular adsorption properties of alpha-Cr2O3, alpha-Fe2O3, and alpha-Al2O3. For the bulk properties, we compared our results for the heat of formation, cohesive energy, lattice parameters and bond distances between the different vdW functionals and available experimental data. Next we studied the adsorption of benzene and CH3 molecules on top of different oxide surfaces. We employed different approximations to exchange and correlation within DFT, namely, the Perdew-Burke-Ernzerhof (PBE) GGA, (PBE)+U, and vdW density functionals [ DFT(vdW-DF/DF2/optPBE/optB86b/optB88)+U] as well as DFT-D2/D3(+U) methods of Grimme for the bulk calculations and optB86b-vdW(+U) and DFT-D2(+U) for the adsorption energy calculations. Our results highlight the importance of vdW interactions not only in the adsorption of molecules, but importantly also for the bulk properties. Although the vdW contribution in the adsorption of CH3 (as a chemisorption interaction) is less important compared to the adsorption of benzene (as a physisorption interaction), this contribution is not negligible. Also adsorption of benzene on ferryl/chromyl terminated surfaces shows an important chemisorption contribution in which the vdW interactions become less significant.
Keywords: A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.123
Times cited: 6
DOI: 10.1039/c6cp00346j
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“How the alignment of adsorbed ortho H pairs determines the onset of selective carbon nanotube etching”. Khalilov U, Bogaerts A, Xu B, Kato T, Kaneko T, Neyts EC, Nanoscale 9, 1653 (2017). http://doi.org/10.1039/C6NR08005G
Abstract: Unlocking the enormous technological potential of carbon nanotubes strongly depends on our ability to specifically produce metallic or semiconducting tubes. While selective etching of both has already been demonstrated, the underlying reasons, however, remain elusive as yet. We here present computational and experimental evidence on the operative mechanisms at the atomic scale. We demonstrate that during the adsorption of H atoms and their coalescence, the adsorbed ortho hydrogen pairs on single-walled carbon nanotubes induce higher shear stresses than axial stresses, leading to the elongation of HC–CH bonds as a function of their alignment with the tube chirality vector, which we denote as the γ-angle. As a result, the C–C cleavage occurs more rapidly in nanotubes containing ortho H-pairs with a small γ-angle. This phenomenon can explain the selective etching of small-diameter semiconductor nanotubes with a similar curvature. Both theoretical and experimental results strongly indicate the important role of the γ-angle in the selective etching mechanisms of carbon nanotubes, in addition to the nanotube curvature and metallicity effects and lead us to clearly understand the onset of selective synthesis/removal of CNT-based materials.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 7.367
Times cited: 6
DOI: 10.1039/C6NR08005G
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“Nanoscale mechanisms of CNT growth and etching in plasma environment”. Khalilov U, Bogaerts A, Hussain S, Kovacevic E, Brault P, Boulmer-Leborgne C, Neyts EC, Journal of physics: D: applied physics 50, 184001 (2017). http://doi.org/10.1088/1361-6463/aa6733
Abstract: Plasma-enhanced chemical deposition (PECVD) of carbon nanotubes has already been shown to allow chirality control to some extent. In PECVD, however, etching may occur simultaneously with the growth, and the occurrence of intermediate processes further significantly complicates the growth process.
We here employ a computational approach with experimental support to study the plasma-based formation of Ni nanoclusters, Ni-catalyzed CNT growth and subsequent etching processes, in order to understand the underpinning nanoscale mechanisms. We find that hydrogen is the dominant factor in both the re-structuring of a Ni film and the subsequent appearance of Ni nanoclusters, as well as in the CNT nucleation and etching processes. The obtained results are compared with available theoretical and experimental studies and provide a deeper understanding of the occurring nanoscale mechanisms in plasma-assisted CNT nucleation and growth.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.588
Times cited: 6
DOI: 10.1088/1361-6463/aa6733
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“Understanding the Effect of Iodide Ions on the Morphology of Gold Nanorods”. Amini MN, Altantzis T, Lobato I, Grzelczak M, Sánchez-Iglesias A, Van Aert S, Liz-Marzán LM, Partoens B, Bals S, Neyts EC, Particle and particle systems characterization 35, 1800051 (2018). http://doi.org/10.1002/ppsc.201800051
Abstract: The presence of iodide ions during the growth of gold nanorods strongly affects the shape of the final products, which is proposed to be due to selective iodide adsorption on certain crystallographic facets. Therefore, a detailed structural and morphological characterization of the starting rods is crucial toward understanding this effect. Electron tomography is used to determine the crystallographic indices of the lateral facets of gold nanorods, as well as those present at the tips. Based on this information, density functional theory calculations are used to determine the surface and interface energies of the observed facets and provide insight into the relationship between the amount of iodide ions in the growth solution and the final morphology of anisotropic gold nanoparticles.
Keywords: A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT); Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.474
Times cited: 6
DOI: 10.1002/ppsc.201800051
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“Mechanisms of Peptide Oxidation by Hydroxyl Radicals: Insight at the Molecular Scale”. Verlackt CCW, Van Boxem W, Dewaele D, Lemière F, Sobott F, Benedikt J, Neyts EC, Bogaerts A, The journal of physical chemistry: C : nanomaterials and interfaces 121, 5787 (2017). http://doi.org/10.1021/acs.jpcc.6b12278
Abstract: Molecular dynamics (MD) simulations were performed to provide atomic scale insight in the initial interaction between hydroxyl radicals (OH) and peptide systems in solution. These OH radicals are representative reactive oxygen species produced by cold atmospheric plasmas. The use of plasma for biomedical applications is gaining increasing interest, but the fundamental mechanisms behind the plasma modifications still remain largely elusive. This study helps to gain more insight in the underlying mechanisms of plasma medicine but is also more generally applicable to peptide oxidation, of interest for other applications. Combining both reactive and nonreactive MD simulations, we are able to elucidate the reactivity of the amino acids inside the peptide systems and their effect on their structure up to 1 μs. Additionally, experiments were performed, treating the simulated peptides with a plasma jet. The computational results presented here correlate well with the obtained experimental data and highlight the importance of the chemical environment for the reactivity of the individual amino acids, so that specific amino acids are attacked in higher numbers than expected. Furthermore, the long time scale simulations suggest that a single oxidation has an effect on the 3D conformation due to an increase in hydrophilicity and intra- and intermolecular interactions.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
Times cited: 5
DOI: 10.1021/acs.jpcc.6b12278
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“Toward the Understanding of Selective Si Nano-Oxidation by Atomic Scale Simulations”. Khalilov U, Bogaerts A, Neyts EC, Accounts of chemical research 50, 796 (2017). http://doi.org/10.1021/acs.accounts.6b00564
Abstract: The continuous miniaturization of nanodevices, such as transistors, solar cells, and optical fibers, requires the controlled synthesis of (ultra)thin gate oxides (<10 nm), including Si gate-oxide (SiO2) with high quality at the atomic scale. Traditional thermal growth of SiO2 on planar Si surfaces, however, does not allow one to obtain such ultrathin oxide due to either the high oxygen diffusivity at high temperature or the very low sticking ability of incident oxygen at low temperature. Two recent techniques, both operative at low (room) temperature, have been put forward to overcome these obstacles: (i) hyperthermal oxidation of planar Si surfaces and (ii) thermal or plasma-assisted oxidation of nonplanar Si surfaces, including Si nanowires (SiNWs). These nanooxidation processes are, however, often difficult to study experimentally, due to the key intermediate processes taking place on the nanosecond time scale.
In this Account, these Si nano-oxidation techniques are discussed from a computational point of view and compared to both hyperthermal and thermal oxidation experiments, as well as to well-known models of thermal oxidation, including the Deal−Grove, Cabrera−Mott, and Kao models and several alternative mechanisms. In our studies, we use reactive molecular dynamics (MD) and hybrid MD/Monte Carlo simulation techniques, applying the Reax force field. The incident energy of oxygen species is chosen in the range of 1−5 eV in hyperthermal oxidation of planar Si surfaces in order to prevent energy-induced damage. It turns out that hyperthermal growth allows for two growth modes, where the ultrathin oxide thickness depends on either (1) only the kinetic energy of the incident oxygen species at a growth temperature below Ttrans = 600 K, or (2) both the incident energy and the growth temperature at a growth temperature above Ttrans. These modes are specific to such ultrathin oxides, and are not observed in traditional thermal oxidation, nor theoretically considered by already existing models. In the case of thermal or plasma-assisted oxidation of small Si nanowires, on the other hand, the thickness of the ultrathin oxide is a function of the growth temperature and the nanowire diameter. Below Ttrans, which varies with the nanowire diameter, partially oxidized SiNW are formed, whereas complete oxidation to a SiO2 nanowire occurs only above Ttrans. In both nano-oxidation processes at lower temperature (T < Ttrans), final sandwich c-Si|SiOx|a-SiO2 structures are obtained due to a competition between overcoming the energy barrier to penetrate into Si subsurface layers and the compressive stress (∼2−3 GPa) at the Si crystal/oxide interface. The overall atomic-simulation results strongly indicate that the thickness of the intermediate SiOx (x < 2) region is very limited (∼0.5 nm) and constant irrespective of oxidation parameters. Thus, control over the ultrathin SiO2 thickness with good quality is indeed possible by accurately tuning the oxidant energy, oxidation temperature and surface curvature.
In general, we discuss and put in perspective these two oxidation mechanisms for obtaining controllable ultrathin gate-oxide films, offering a new route toward the fabrication of nanodevices via selective nano-oxidation.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 20.268
Times cited: 5
DOI: 10.1021/acs.accounts.6b00564
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“Density functional theory study of interface interactions in hydroxyapatite/rutile composites for biomedical applications”. Grubova IY, Surmeneva MA, Huygh S, Surmenev RA, Neyts EC, The journal of physical chemistry: C : nanomaterials and interfaces 121, 15687 (2017). http://doi.org/10.1021/ACS.JPCC.7B02926
Abstract: To gain insight into the nature of the adhesion mechanism between hydroxyapatite (HA) and rutile (rTiO(2)), the mutual affinity between their surfaces was systematically studied using density functional theory (DFT). We calculated both bulk and surface properties of HA and rTiO(2), and explored the interfacial bonding mechanism of amorphous HA (aHA) surface onto amorphous as well as stoichiometric and nonstoichiometric crystalline rTiO(2). Formation energies of bridging and subbridging oxygen vacancies considered in the rTiO(2)(110) surface were evaluated and compared with other theoretical and experimental results. The interfacial interaction was evaluated through the work of adhesion. For the aHA/rTiO(2)(110) interfaces, the work of adhesion is found to depend strongly on the chemical environment of the rTiO(2)(110) surface. Electronic analysis indicates that the charge transfer is very small in the case of interface formation between aHA and crystalline rTiO(2)(110). In contrast, significant charge transfer occurs between aHA and amorphous rTiO(2) (aTiO(2)) slabs during the formation of the interface. Charge density difference (CDD) analysis indicates that the dominant interactions in the interface have significant covalent character, and in particular the Ti-O and Ca-O bonds. Thus, the obtained results reveal that the aHA/aTiO(2) interface shows a more preferable interaction and is thermodynamically more stable than other interfaces. These results are particularly important for improving the long-term stability of HA-based implants.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
Times cited: 5
DOI: 10.1021/ACS.JPCC.7B02926
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“Atomistic simulations of plasma catalytic processes”. Neyts EC, Frontiers of Chemical Science and Engineering 12, 145 (2018). http://doi.org/10.1007/S11705-017-1674-7
Abstract: There is currently a growing interest in the realisation and optimization of hybrid plasma/catalyst systems for a multitude of applications, ranging from nanotechnology to environmental chemistry. In spite of this interest, there is, however, a lack in fundamental understanding of the underlying processes in such systems. While a lot of experimental research is already being carried out to gain this understanding, only recently the first simulations have appeared in the literature. In this contribution, an overview is presented on atomic scale simulations of plasma catalytic processes as carried out in our group. In particular, this contribution focusses on plasma-assisted catalyzed carbon nanostructure growth, and plasma catalysis for greenhouse gas conversion. Attention is paid to what can routinely be done, and where challenges persist.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 1.712
Times cited: 5
DOI: 10.1007/S11705-017-1674-7
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“Overcoming Old Scaling Relations and Establishing New Correlations in Catalytic Surface Chemistry: Combined Effect of Charging and Doping”. Bal KM, Neyts EC, The journal of physical chemistry: C : nanomaterials and interfaces 123, 6141 (2019). http://doi.org/10.1021/acs.jpcc.9b01216
Abstract: Optimization of catalytic materials for a given application is greatly constrained by linear scaling relations. Recently, however, it has been demonstrated that it is possible to reversibly modulate the chemisorption of molecules on nanomaterials by charging (i.e., injection or removal of electrons) and hence reversibly and selectively modify catalytic activity beyond structure−activity correlations. The fundamental physical relation between the properties of the material, the charging process, and the chemisorption energy, however, remains unclear, and a systematic exploration and optimization of charge-switchable sorbent materials is not yet possible. Using hybrid DFT calculations of CO2 chemisorption on hexagonal boron nitride nanosheets with several types of defects and dopants, we here reveal the existence of fundamental correlations between the electron affinity of a material and charge-induced chemisorption, show how defect engineering can be used to modulate the strength and efficiency of the adsorption process, and demonstrate that excess electrons stabilize many topological defects. We then show how these insights could be exploited in the development of new electrocatalytic materials and the synthesis of doped nanomaterials. Moreover, we demonstrate that calculated chemical properties of charged materials are highly sensitive to the employed computational methodology because of the self-interaction error, which underlines the theoretical challenge posed by such systems.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
Times cited: 5
DOI: 10.1021/acs.jpcc.9b01216
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