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Bathellier A, Moreno D, Maron L, Dinoi C, Rosal I. Grafting of Lanthanum Complexes on a Functionalized Graphene Surface: Theoretical Investigation on Ethylene and 1,3‐Butadiene Homo‐ and Co‐Polymerization. Chemistry 2020; 26:13213-13225. [DOI: 10.1002/chem.202001056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Indexed: 11/08/2022]
Affiliation(s)
- Adrien Bathellier
- INSA, UPS, CNRS (UMR 5215), Institut National des, Sciences Appliquées, LPCNO (IRSAMC) Université de Toulouse 135 avenue de Rangueil 31077 Toulouse France
| | - Diego Moreno
- INSA, UPS, CNRS (UMR 5215), Institut National des, Sciences Appliquées, LPCNO (IRSAMC) Université de Toulouse 135 avenue de Rangueil 31077 Toulouse France
| | - Laurent Maron
- INSA, UPS, CNRS (UMR 5215), Institut National des, Sciences Appliquées, LPCNO (IRSAMC) Université de Toulouse 135 avenue de Rangueil 31077 Toulouse France
| | - Chiara Dinoi
- INSA, UPS, CNRS (UMR 5215), Institut National des, Sciences Appliquées, LPCNO (IRSAMC) Université de Toulouse 135 avenue de Rangueil 31077 Toulouse France
| | - Iker Rosal
- INSA, UPS, CNRS (UMR 5215), Institut National des, Sciences Appliquées, LPCNO (IRSAMC) Université de Toulouse 135 avenue de Rangueil 31077 Toulouse France
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2
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Grajciar L, Heard CJ, Bondarenko AA, Polynski MV, Meeprasert J, Pidko EA, Nachtigall P. Towards operando computational modeling in heterogeneous catalysis. Chem Soc Rev 2018; 47:8307-8348. [PMID: 30204184 PMCID: PMC6240816 DOI: 10.1039/c8cs00398j] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Indexed: 12/19/2022]
Abstract
An increased synergy between experimental and theoretical investigations in heterogeneous catalysis has become apparent during the last decade. Experimental work has extended from ultra-high vacuum and low temperature towards operando conditions. These developments have motivated the computational community to move from standard descriptive computational models, based on inspection of the potential energy surface at 0 K and low reactant concentrations (0 K/UHV model), to more realistic conditions. The transition from 0 K/UHV to operando models has been backed by significant developments in computer hardware and software over the past few decades. New methodological developments, designed to overcome part of the gap between 0 K/UHV and operando conditions, include (i) global optimization techniques, (ii) ab initio constrained thermodynamics, (iii) biased molecular dynamics, (iv) microkinetic models of reaction networks and (v) machine learning approaches. The importance of the transition is highlighted by discussing how the molecular level picture of catalytic sites and the associated reaction mechanisms changes when the chemical environment, pressure and temperature effects are correctly accounted for in molecular simulations. It is the purpose of this review to discuss each method on an equal footing, and to draw connections between methods, particularly where they may be applied in combination.
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Affiliation(s)
- Lukáš Grajciar
- Department of Physical and Macromolecular Chemistry
, Faculty of Science
, Charles University in Prague
,
128 43 Prague 2
, Czech Republic
.
;
;
| | - Christopher J. Heard
- Department of Physical and Macromolecular Chemistry
, Faculty of Science
, Charles University in Prague
,
128 43 Prague 2
, Czech Republic
.
;
;
| | - Anton A. Bondarenko
- TheoMAT group
, ITMO University
,
Lomonosova 9
, St. Petersburg
, 191002
, Russia
| | - Mikhail V. Polynski
- TheoMAT group
, ITMO University
,
Lomonosova 9
, St. Petersburg
, 191002
, Russia
| | - Jittima Meeprasert
- Inorganic Systems Engineering group
, Department of Chemical Engineering
, Faculty of Applied Sciences
, Delft University of Technology
,
Van der Maasweg 9
, 2629 HZ Delft
, The Netherlands
.
| | - Evgeny A. Pidko
- TheoMAT group
, ITMO University
,
Lomonosova 9
, St. Petersburg
, 191002
, Russia
- Inorganic Systems Engineering group
, Department of Chemical Engineering
, Faculty of Applied Sciences
, Delft University of Technology
,
Van der Maasweg 9
, 2629 HZ Delft
, The Netherlands
.
| | - Petr Nachtigall
- Department of Physical and Macromolecular Chemistry
, Faculty of Science
, Charles University in Prague
,
128 43 Prague 2
, Czech Republic
.
;
;
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Sun X, Han P, Li B, Mao S, Liu T, Ali S, Lian Z, Su D. Oxidative dehydrogenation reaction of short alkanes on nanostructured carbon catalysts: a computational account. Chem Commun (Camb) 2018; 54:864-875. [DOI: 10.1039/c7cc06941c] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We aim to provide an overview of the current status and recent achievements of computational studies of the ODH reaction on nanostructured carbon catalysts.
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Affiliation(s)
- XiaoYing Sun
- Institute of Catalysis for Energy and Environment
- College of Chemistry and Chemical Engineering
- Shenyang Normal University
- Shenyang 110034
- China
| | - Peng Han
- Institute of Catalysis for Energy and Environment
- College of Chemistry and Chemical Engineering
- Shenyang Normal University
- Shenyang 110034
- China
| | - Bo Li
- Shenyang National Laboratory for Materials Science
- Institute of Metal Research
- Chinese Academy of Sciences
- Shenyang 110016
- China
| | - ShanJun Mao
- Shenyang National Laboratory for Materials Science
- Institute of Metal Research
- Chinese Academy of Sciences
- Shenyang 110016
- China
| | - TianFu Liu
- Shenyang National Laboratory for Materials Science
- Institute of Metal Research
- Chinese Academy of Sciences
- Shenyang 110016
- China
| | - Sajjad Ali
- Shenyang National Laboratory for Materials Science
- Institute of Metal Research
- Chinese Academy of Sciences
- Shenyang 110016
- China
| | - Zan Lian
- Shenyang National Laboratory for Materials Science
- Institute of Metal Research
- Chinese Academy of Sciences
- Shenyang 110016
- China
| | - DangSheng Su
- Shenyang National Laboratory for Materials Science
- Institute of Metal Research
- Chinese Academy of Sciences
- Shenyang 110016
- China
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4
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Brunk E, Rothlisberger U. Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States. Chem Rev 2015; 115:6217-63. [PMID: 25880693 DOI: 10.1021/cr500628b] [Citation(s) in RCA: 301] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Elizabeth Brunk
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,‡Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94618, United States
| | - Ursula Rothlisberger
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,§National Competence Center of Research (NCCR) MARVEL-Materials' Revolution: Computational Design and Discovery of Novel Materials, 1015 Lausanne, Switzerland
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Mulet-Gas M, Abella L, Dunk PW, Rodríguez-Fortea A, Kroto HW, Poblet JM. Small endohedral metallofullerenes: exploration of the structure and growth mechanism in the Ti@C 2n (2 n = 26-50) family. Chem Sci 2014; 6:675-686. [PMID: 28936315 PMCID: PMC5590485 DOI: 10.1039/c4sc02268h] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 09/12/2014] [Indexed: 12/02/2022] Open
Abstract
Analysis of the structure and the bottom-up growth mechanism in the family of small endohedral metallofullerenes Ti@C2n (2n = 26–50).
The formation of the smallest fullerene, C28, was recently reported using gas phase experiments combined with high-resolution FT-ICR mass spectrometry. An internally located group IV metal stabilizes the highly strained non-IPR C28 cage by charge transfer (IPR = isolated pentagon rule). Ti@C44 also appeared as a prominent peak in the mass spectra, and U@C28 was demonstrated to form by a bottom-up growth mechanism. We report here a computational analysis using standard DFT calculations and Car–Parrinello MD simulations for the family of the titled compounds, aiming to identify the optimal cage for each endohedral fullerene and to unravel key aspects of the intriguing growth mechanisms of fullerenes. We show that all the optimal isomers from C26 to C50 are linked by a simple C2 insertion, with the exception of a few carbon cages that require an additional C2 rearrangement. The ingestion of a C2 unit is always an exergonic/exothermic process that can occur through a rather simple mechanism, with the most energetically demanding step corresponding to the closure of the carbon cage. The large formation abundance observed in mass spectra for Ti@C28 and Ti@C44 can be explained by the special electronic properties of these cages and their higher relative stabilities with respect to C2 reactivity. We further verify that extrusion of C atoms from an already closed fullerene is much more energetically demanding than forming the fullerene by a bottom-up mechanism. Independent of the formation mechanism, the present investigations strongly support that, among all the possible isomers, the most stable, smaller non-IPR carbon cages are formed, a conclusion that is also valid for medium and large cages.
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Affiliation(s)
- Marc Mulet-Gas
- Departament de Química Física i Inorgànica , Universitat Rovira i Virgili , Marcellí Domingo s/n , 43007 Tarragona , Spain . ;
| | - Laura Abella
- Departament de Química Física i Inorgànica , Universitat Rovira i Virgili , Marcellí Domingo s/n , 43007 Tarragona , Spain . ;
| | - Paul W Dunk
- Department of Chemistry and Biochemistry , Florida State University , Tallahassee , Florida 32306 , USA .
| | - Antonio Rodríguez-Fortea
- Departament de Química Física i Inorgànica , Universitat Rovira i Virgili , Marcellí Domingo s/n , 43007 Tarragona , Spain . ;
| | - Harold W Kroto
- Department of Chemistry and Biochemistry , Florida State University , Tallahassee , Florida 32306 , USA .
| | - Josep M Poblet
- Departament de Química Física i Inorgànica , Universitat Rovira i Virgili , Marcellí Domingo s/n , 43007 Tarragona , Spain . ;
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Zheng S, Pfaendtner J. Enhanced sampling of chemical and biochemical reactions with metadynamics. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.923574] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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7
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Solvation structure and dynamics of Li+ ion in liquid water, methanol and ethanol: A comparison study. Chem Phys 2014. [DOI: 10.1016/j.chemphys.2014.02.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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8
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Car–Parrinello molecular dynamics simulations of Na+ solvation in water, methanol and ethanol. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.04.035] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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9
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Gerber I, Oubenali M, Bacsa R, Durand J, Gonçalves A, Pereira MFR, Jolibois F, Perrin L, Poteau R, Serp P. Theoretical and Experimental Studies on the Carbon-Nanotube Surface Oxidation by Nitric Acid: Interplay between Functionalization and Vacancy Enlargement. Chemistry 2011; 17:11467-77. [DOI: 10.1002/chem.201101438] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Indexed: 11/11/2022]
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Vilà-Nadal L, Wilson EF, Miras HN, Rodríguez-Fortea A, Cronin L, Poblet JM. Combined Theoretical and Mass Spectrometry Study of the Formation-Fragmentation of Small Polyoxomolybdates. Inorg Chem 2011; 50:7811-9. [DOI: 10.1021/ic200969h] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Laia Vilà-Nadal
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, c/Marcel·lí Domingo s/n, 43007 Tarragona, Spain
| | - Elizabeth F. Wilson
- School of Chemistry, The University of Glasgow, University Avenue, Glasgow G12 8QQ, Scotland, U.K
| | - Haralampos N. Miras
- School of Chemistry, The University of Glasgow, University Avenue, Glasgow G12 8QQ, Scotland, U.K
| | - Antonio Rodríguez-Fortea
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, c/Marcel·lí Domingo s/n, 43007 Tarragona, Spain
| | - Leroy Cronin
- School of Chemistry, The University of Glasgow, University Avenue, Glasgow G12 8QQ, Scotland, U.K
| | - Josep M. Poblet
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, c/Marcel·lí Domingo s/n, 43007 Tarragona, Spain
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Vilà-Nadal L, Mitchell SG, Rodríguez-Fortea A, Miras HN, Cronin L, Poblet JM. Connecting theory with experiment to understand the initial nucleation steps of heteropolyoxometalate clusters. Phys Chem Chem Phys 2011; 13:20136-45. [DOI: 10.1039/c1cp21209e] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Vilà -Nadal L, RodrÃguez-Fortea A, Poblet JM. Theoretical Analysis of the Possible Intermediates in the Formation of [W6O19]2â. Eur J Inorg Chem 2009. [DOI: 10.1002/ejic.200900714] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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14
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Park J, Lin MC. Thermal Decomposition of Gaseous Ammonium Nitrate at Low Pressure: Kinetic Modeling of Product Formation and Heterogeneous Decomposition of Nitric Acid. J Phys Chem A 2009; 113:13556-61. [DOI: 10.1021/jp9058005] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- J. Park
- Department of Chemistry, Emory University, Atlanta, Georgia 30322
| | - M. C. Lin
- Department of Chemistry, Emory University, Atlanta, Georgia 30322
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15
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Popovicheva OB, Kireeva ED, Shonija NK, Khokhlova TD. Water Interaction with Laboratory-Simulated Fossil Fuel Combustion Particles. J Phys Chem A 2009; 113:10503-11. [DOI: 10.1021/jp905522s] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- O. B. Popovicheva
- Institute of Nuclear Physics and Chemical Department, Moscow State University, 119991 Moscow, Russia
| | - E. D. Kireeva
- Institute of Nuclear Physics and Chemical Department, Moscow State University, 119991 Moscow, Russia
| | - N. K. Shonija
- Institute of Nuclear Physics and Chemical Department, Moscow State University, 119991 Moscow, Russia
| | - T. D. Khokhlova
- Institute of Nuclear Physics and Chemical Department, Moscow State University, 119991 Moscow, Russia
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16
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Petersen L, Ardèvol A, Rovira C, Reilly PJ. Mechanism of Cellulose Hydrolysis by Inverting GH8 Endoglucanases: A QM/MM Metadynamics Study. J Phys Chem B 2009; 113:7331-9. [DOI: 10.1021/jp811470d] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luis Petersen
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Albert Ardèvol
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Carme Rovira
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Peter J. Reilly
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
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Rodríguez-Fortea A, Vilà-Nadal L, Poblet JM. Hydration of Hydrogentungstate Anions at Different pH Conditions: A Car−Parrinello Molecular Dynamics Study. Inorg Chem 2008; 47:7745-50. [DOI: 10.1021/ic8007766] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Antonio Rodríguez-Fortea
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, C/Marcel·lí Domingo s/n, 43007 Tarragona, Spain
| | - Laia Vilà-Nadal
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, C/Marcel·lí Domingo s/n, 43007 Tarragona, Spain
| | - Josep M. Poblet
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, C/Marcel·lí Domingo s/n, 43007 Tarragona, Spain
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Urakawa A, Iannuzzi M, Hutter J, Baiker A. Towards a Rational Design of Ruthenium CO2 Hydrogenation Catalysts by Ab Initio Metadynamics. Chemistry 2007; 13:6828-40. [PMID: 17566132 DOI: 10.1002/chem.200700254] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Complete reaction pathways relevant to CO2 hydrogenation by using a homogeneous ruthenium dihydride catalyst ([Ru(dmpe)2H2], dmpe=Me2PCH2CH2PMe2) have been investigated by ab initio metadynamics. This approach has allowed reaction intermediates to be identified and free-energy profiles to be calculated, which provide new insights into the experimentally observed reaction pathway. Our simulations indicate that CO2 insertion, which leads to the formation of formate complexes, proceeds by a concerted insertion mechanism. It is a rapid and direct process with a relatively low activation barrier, which is in agreement with experimental observations. Subsequent H2 insertion into the formate--Ru complex, which leads to the formation of formic acid, instead occurs via an intermediate [Ru(eta2-H2)] complex in which the molecular hydrogen coordinates to the ruthenium center and interacts weakly with the formate group. This step has been identified as the rate-limiting step. The reaction completes by hydrogen transfer from the [Ru(eta2-H2)] complex to the formate oxygen atom, which forms a dihydrogen-bonded Ru--HHO(CHO) complex. The activation energy for the H2 insertion step is lower for the trans isomer than for the cis isomer. A simple measure of the catalytic activity was proposed based on the structure of the transition state of the identified rate-limiting step. From this measure, the relationship between catalysts with different ligands and their experimental catalytic activities can be explained.
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Affiliation(s)
- Atsushi Urakawa
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Hönggerberg, HCI 8093 Zurich, Switzerland
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Abstract
Heterocycles' aggregates show rather good proton conductivity. In particular, condensed structures formed by imidazole rings that are held together by polymeric chains have attracted some interest as possible candidate materials for fuel cell membranes. However, the details of the proton diffusion process could not be resolved by means of experimental measurements because of the fast rearrangement of the structure after each proton exchange. In this work, we report in detail the results of ab initio molecular dynamics calculations, which were briefly presented in a previous Letter [M. Iannuzzi and M. Parrinello, Phys. Rev. Lett. 93, 025901 (2004)]. The conformational changes associated with the diffusion of protons in model crystalline structures containing chains of imidazole rings are described in the framework of an atomistic approach. In particular, the bonding pattern characterizing the structure of imidazole-2-ethylene-oxide doped by an excess proton is also studied through the calculation of the 1H NMR chemical shifts. The unresolved resonances appearing in the experimental spectra could be associated with specific structural features, in connection with the fluctuating hydrogen bonding. The analysis of the distortions that induce or are induced by the mobility of the protons offers some new hints for the engineering of new proton conducting materials.
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Affiliation(s)
- Marcella Iannuzzi
- Physical Chemistry Institute, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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