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Rapacioli M, Buey MY, Spiegelman F. Addressing electronic and dynamical evolution of molecules and molecular clusters: DFTB simulations of energy relaxation in polycyclic aromatic hydrocarbons. Phys Chem Chem Phys 2024; 26:1499-1515. [PMID: 37933901 PMCID: PMC10793726 DOI: 10.1039/d3cp02852f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/17/2023] [Indexed: 11/08/2023]
Abstract
We present a review of the capabilities of the density functional based Tight Binding (DFTB) scheme to address the electronic relaxation and dynamical evolution of molecules and molecular clusters following energy deposition via either collision or photoabsorption. The basics and extensions of DFTB for addressing these systems and in particular their electronic states and their dynamical evolution are reviewed. Applications to PAH molecules and clusters, carbonaceous systems of major interest in astrochemical/astrophysical context, are reported. A variety of processes are examined and discussed such as collisional hydrogenation, fast collisional processes and induced electronic and charge dynamics, collision-induced fragmentation, photo-induced fragmentation, relaxation in high electronic states, electronic-to-vibrational energy conversion and statistical versus non-statistical fragmentation. This review illustrates how simulations may help to unravel different relaxation mechanisms depending on various factors such as the system size, specific electronic structure or excitation conditions, in close connection with experiments.
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Affiliation(s)
- Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantique (LCPQ/FERMI), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
| | - Maysa Yusef Buey
- Laboratoire de Chimie et Physique Quantique (LCPQ/FERMI), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
| | - Fernand Spiegelman
- Laboratoire de Chimie et Physique Quantique (LCPQ/FERMI), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
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Yusef Buey M, Mineva T, Rapacioli M. Coupling density functional based tight binding with class 1 force fields in a hybrid QM/MM scheme. Theor Chem Acc 2022. [DOI: 10.1007/s00214-022-02878-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Zheng L, Cuny J, Zamith S, L'Hermite JM, Rapacioli M. Collision-induced dissociation of protonated uracil water clusters probed by molecular dynamics simulations. Phys Chem Chem Phys 2021; 23:27404-27416. [PMID: 34859809 DOI: 10.1039/d1cp03228c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Collision-induced dissociation experiments of hydrated molecular species can provide a wealth of important information. However, they often need a theoretical support to extract chemical information. In the present article, in order to provide a detailed description of recent experimental measurements [Braud et al., J. Chem. Phys., 2019, 150, 014303], collision simulations between low-energy protonated uracil water clusters (H2O)1-7,11,12UH+ and an Ar atom were performed using a quantum mechanics/molecular mechanics formalism based on the self-consistent-charge density-functional based tight-binding method. The theoretical proportion of formed neutral vs. protonated uracil containing clusters, total fragmentation cross sections as well as the mass spectra of charged fragments are consistent with the experimental data which highlights the accuracy of the present simulations. They allow to probe which fragments are formed on the short time scale and rationalize the location of the excess proton on these fragments. We demonstrate that this latter property is highly influenced by the nature of the aggregate undergoing the collision. Analyses of the time evolution of the fragments populations and of their relative abundances demonstrate that, up to 7 water molecules, a direct dissociation mechanism occurs after collision whereas for 11 and 12 water molecules a statistical mechanism is more likely to participate. Although scarce in the literature, the present simulations appear as a useful tool to complement collision-induced dissociation experiments of hydrated molecular species.
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Affiliation(s)
- Linjie Zheng
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
| | - Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
| | - Sébastien Zamith
- Laboratoire Collisions Agrégats Réactivié LCAR/IRSAMC, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Jean-Marc L'Hermite
- Laboratoire Collisions Agrégats Réactivié LCAR/IRSAMC, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
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Miyazaki M, Sakata Y, Ono M, Otsuka R, Ohara R, Dopfer O, Fujii M. Isomer-Selective Spectroscopy and Dynamics of Phenol-Ar n ( n ≤ 5) Clusters. J Phys Chem A 2021; 125:9969-9981. [PMID: 34761924 DOI: 10.1021/acs.jpca.1c04815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Structures and ionization-induced solvation dynamics of phenol-(argon)n clusters, PhOH-Arn (n ≤ 5), were studied by using a variety of isomer-selective photoionization and vibrational spectroscopic techniques. Several higher-energy isomers were found and assigned for the first time by systematically controlling the experimental conditions of the supersonic expansion. This behavior is also confirmed for the PhOH-Kr2 cluster. Solvation structures are elucidated by evaluating systematic shifts in the S1 ← S0 origin and ionization energies obtained by resonance-enhanced photoionization, in addition to the OH stretching frequency obtained by IR photodissociation. Isomer-selective picosecond time-resolved IR spectroscopy for the n = 2 clusters revealed that the dynamics for the ionization-induced intermolecular π → H site-switching reaction strongly depends on the initial isomeric structure. In particular, the reaction time for the (1|1) isomer is 7 ps, while that for (2|0) is <3 ps. This difference shows that the switching time is determined by the distance of the reaction coordinate between the initial π-site and the final OH-site.
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Affiliation(s)
- Mitsuhiko Miyazaki
- Natural Science Division, Faculty of Core Research, Ochanomizu University, Tokyo 112-8610, Japan.,Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Yuri Sakata
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Megumi Ono
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Remina Otsuka
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Ryuhei Ohara
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, 10623 Berlin, Germany.,World Research Hub Initiatives, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan.,World Research Hub Initiatives, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
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Dontot L, Spiegelman F, Zamith S, Rapacioli M. Dependence upon charge of the vibrational spectra of small Polycyclic Aromatic Hydrocarbon clusters: the example of pyrene. THE EUROPEAN PHYSICAL JOURNAL. D, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 2020; 74:216. [PMID: 33597829 PMCID: PMC7116754 DOI: 10.1140/epjd/e2020-10081-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 07/18/2020] [Accepted: 09/01/2020] [Indexed: 06/12/2023]
Abstract
Infrared spectra are computed for neutral and cationic clusters of Polycyclic Aromatic Hydrocarbon clusters, namely( C 16 H 10 ) n = 1 , 4 ( 0 / + ) , using the Density Functional based Tight Binding scheme combined with a Configuration Interaction scheme (DFTB-CI) in the double harmonic approximation. Cross-comparison is carried out with DFT and simple DFTB. Similarly to the monomer cation, the IR spectra of cluster cations are characterized by a depletion of the intensity of the CH stretch modes around 3000 cm-1, with a weak revival for n = 3 and 4. The in-plane CCC modes in the region 1400-2000 cm-1 are enhanced while the CH bending modes in the range 700-1000 cm-1 are significantly weakened with respect to the monomer cation, in particular for n = 2. Finally, soft modes corresponding to diedral fluctuations of the monomers within the central stack of the ion structure, possibly mixed with monomer folding, are also observed in the region 70-120 cm-1.
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Affiliation(s)
- Léo Dontot
- Laboratoire de Chimie et Physique Quantique (LCPQ/IRSAMC), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Fernand Spiegelman
- Laboratoire de Chimie et Physique Quantique (LCPQ/IRSAMC), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Sébastien Zamith
- Laboratoire Collisions Agrégats Réactivité (LCAR/IRSAMC), UMR5589, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantique (LCPQ/IRSAMC), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
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Spiegelman F, Tarrat N, Cuny J, Dontot L, Posenitskiy E, Martí C, Simon A, Rapacioli M. Density-functional tight-binding: basic concepts and applications to molecules and clusters. ADVANCES IN PHYSICS: X 2020; 5:1710252. [PMID: 33154977 PMCID: PMC7116320 DOI: 10.1080/23746149.2019.1710252] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/19/2019] [Indexed: 06/10/2023] Open
Abstract
The scope of this article is to present an overview of the Density Functional based Tight Binding (DFTB) method and its applications. The paper introduces the basics of DFTB and its standard formulation up to second order. It also addresses methodological developments such as third order expansion, inclusion of non-covalent interactions, schemes to solve the self-interaction error, implementation of long-range short-range separation, treatment of excited states via the time-dependent DFTB scheme, inclusion of DFTB in hybrid high-level/low level schemes (DFT/DFTB or DFTB/MM), fragment decomposition of large systems, large scale potential energy landscape exploration with molecular dynamics in ground or excited states, non-adiabatic dynamics. A number of applications are reviewed, focusing on -(i)- the variety of systems that have been studied such as small molecules, large molecules and biomolecules, bare orfunctionalized clusters, supported or embedded systems, and -(ii)- properties and processes, such as vibrational spectroscopy, collisions, fragmentation, thermodynamics or non-adiabatic dynamics. Finally outlines and perspectives are given.
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Affiliation(s)
- Fernand Spiegelman
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Nathalie Tarrat
- CEMES, Université de Toulouse (UPS), CNRS, UPR8011, Toulouse, Toulouse, France
| | - Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Leo Dontot
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Evgeny Posenitskiy
- Laboratoire Collisions Agrégats et Réactivité LCAR/IRSAMC, UMR5589, Université de Toulouse (UPS) and CNRS, Toulouse, France
| | - Carles Martí
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
- Laboratoire de Chimie, UMR5182, Ecole Normale Supérieure de Lyon, Université de Lyon and CNRS, Lyon, France
| | - Aude Simon
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
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Simon A, Rapacioli M, Michoulier E, Zheng L, Korchagina K, Cuny J. Contribution of the density-functional-based tight-binding scheme to the description of water clusters: methods, applications and extension to bulk systems. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1554903] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- A. Simon
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - M. Rapacioli
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - E. Michoulier
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
- Laboratoire Collisions Agrégats et Réactivité LCAR/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - L. Zheng
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - K. Korchagina
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - J. Cuny
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
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Simon A, Noble JA, Rouaut G, Moudens A, Aupetit C, Iftner C, Mascetti J. Formation of coronene:water complexes: FTIR study in argon matrices and theoretical characterisation. Phys Chem Chem Phys 2017; 19:8516-8529. [DOI: 10.1039/c6cp08559h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coronene preferentially forms σ-type rather than π-type complexes with water in low temperature argon matrices.
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Affiliation(s)
- A. Simon
- Laboratoire de Chimie et Physique Quantiques (LCPQ)
- IRSAMC
- UMR 5626 CNRS & Université Paul Sabatier
- 31062 Toulouse Cedex 09
- France
| | - J. A. Noble
- Institut des Sciences Moléculaires (ISM)
- Université de Bordeaux
- UMR 5255 CNRS
- 33405 Talence cedex
- France
| | - G. Rouaut
- Laboratoire de Chimie et Physique Quantiques (LCPQ)
- IRSAMC
- UMR 5626 CNRS & Université Paul Sabatier
- 31062 Toulouse Cedex 09
- France
| | - A. Moudens
- Institut des Sciences Moléculaires (ISM)
- Université de Bordeaux
- UMR 5255 CNRS
- 33405 Talence cedex
- France
| | - C. Aupetit
- Institut des Sciences Moléculaires (ISM)
- Université de Bordeaux
- UMR 5255 CNRS
- 33405 Talence cedex
- France
| | - C. Iftner
- Laboratoire de Chimie et Physique Quantiques (LCPQ)
- IRSAMC
- UMR 5626 CNRS & Université Paul Sabatier
- 31062 Toulouse Cedex 09
- France
| | - J. Mascetti
- Institut des Sciences Moléculaires (ISM)
- Université de Bordeaux
- UMR 5255 CNRS
- 33405 Talence cedex
- France
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Dontot L, Suaud N, Rapacioli M, Spiegelman F. An extended DFTB-CI model for charge-transfer excited states in cationic molecular clusters: model studies versus ab initio calculations in small PAH clusters. Phys Chem Chem Phys 2016; 18:3545-57. [PMID: 26750534 DOI: 10.1039/c5cp06344b] [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
We present an extension of the constrained density functional tight binding scheme combined with configuration interaction (DFTB-CI) to efficiently compute excited states of molecular cluster cations.
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Affiliation(s)
- Léo Dontot
- Laboratoire de Chimie et de Physique Quantiques (LCPQ)
- IRSAMC
- Université de Toulouse (UPS) and CNRS
- F-31062 Toulouse
- France
| | - Nicolas Suaud
- Laboratoire de Chimie et de Physique Quantiques (LCPQ)
- IRSAMC
- Université de Toulouse (UPS) and CNRS
- F-31062 Toulouse
- France
| | - Mathias Rapacioli
- Laboratoire de Chimie et de Physique Quantiques (LCPQ)
- IRSAMC
- Université de Toulouse (UPS) and CNRS
- F-31062 Toulouse
- France
| | - Fernand Spiegelman
- Laboratoire de Chimie et de Physique Quantiques (LCPQ)
- IRSAMC
- Université de Toulouse (UPS) and CNRS
- F-31062 Toulouse
- France
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Simon A, Iftner C, Mascetti J, Spiegelman F. Water clusters in an argon matrix: infrared spectra from molecular dynamics simulations with a self-consistent charge density functional-based tight binding/force-field potential. J Phys Chem A 2015; 119:2449-67. [PMID: 25650885 DOI: 10.1021/jp508533k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The present theoretical study aims at investigating the effects of an argon matrix on the structures, energetics, dynamics, and infrared (IR) spectra of small water clusters (H2O)n (n = 1-6). The potential energy surface is obtained from a hybrid self-consistent charge density functional-based tight binding/force-field approach (SCC-DFTB/FF) in which the water clusters are treated at the SCC-DFTB level and the matrix is modeled at the FF level by a cluster consisting of ∼340 Ar atoms with a face centered cubic (fcc) structure, namely (H2O)n/Ar. With respect to a pure FF scheme, this allows a quantum description of the molecular system embedded in the matrix, along with all-atom geometry optimization and molecular dynamics (MD) simulations of the (H2O)n/Ar system. Finite-temperature IR spectra are derived from the MD simulations. The SCC-DFTB/FF scheme is first benchmarked on (H2O)Arn clusters against correlated wave function results and DFT calculations performed in the present work, and against FF data available in the literature. Regarding (H2O)n/Ar systems, the geometries of the water clusters are found to adapt to the fcc environment, possibly leading to intermolecular distortion and matrix perturbation. Several energetical quantities are estimated to characterize the water clusters in the matrix. In the particular case of the water hexamer, substitution and insertion energies for the prism, bag, and cage are found to be lower than that for the 6-member ring isomer. Finite-temperature MD simulations show that the water monomer has a quasifree rotation motion at 13 K, in agreement with experimental data. In the case of the water dimer, the only large-amplitude motion is a distortion-rotation intermolecular motion, whereas only vibration motions around the nuclei equilibrium positions are observed for clusters with larger sizes. Regarding the IR spectra, we find that the matrix environment leads to redshifts of the stretching modes and almost no shift of the bending modes. This is in agreement with experimental data. Furthermore, in the case of the water monomer and dimer, the magnitudes of the computed shifts are in fair agreement with the experimental values. The complex case of the water hexamer, which presents several low-energy isomers, is discussed.
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Affiliation(s)
- Aude Simon
- †Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Christophe Iftner
- †Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Joëlle Mascetti
- ‡Institut des Sciences Moléculaires, Université de Bordeaux and CNRS, 351 Cours de la Libération, 33405 Talence cedex, France
| | - Fernand Spiegelman
- †Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
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Zhang X, Gong X. Theoretical investigation of rare gas adsorption on and inside B-doped carbon nanotubes by DFT, QTAIM and NBO. RSC Adv 2015. [DOI: 10.1039/c5ra10657e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Structures and intramolecular interactions of complexes formed by 1–2 boron atom doped CNTs with rare gases were studied.
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Affiliation(s)
- Xueli Zhang
- School of Chemical Engineering
- Nanjing University of Science and Technology
- Nanjing 210094
- China
| | - Xuedong Gong
- School of Chemical Engineering
- Nanjing University of Science and Technology
- Nanjing 210094
- China
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