J. Ze?evi?, G. Vanbutsele, K. P. Jong, and . De,

J. A. Martens, Nanoscale Intimacy in Bifunctional Catalysts for Selective Conversion of Hydrocarbons, Nature, vol.528, pp.245-248, 2015.

C. Marcilly, Acido-Basic Catalysis. Application to Refining and Petrochemistry

. Technip, , 2005.

E. Gutierrez-acebo, C. Leroux, C. Chizallet, Y. Schuurman, and C. Bouchy, Metal/Acid Bifunctional Catalysis and Intimacy Criterion for Ethylcyclohexane Hydroconversion, ACS Catal, vol.8, pp.6035-6046, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01864958

J. A. Martens, D. Verboekend, K. Thomas, G. Vanbutsele, and J. Gilson,

J. Ramírez, Hydroisomerization of Emerging Renewable Hydrocarbons Using Hierarchical Pt/H-ZSM-22 Catalyst, ChemSusChem, vol.6, pp.421-425, 2013.

P. A. Jacobs, M. Dusselier, and B. F. Sels, Will Zeolite-Based Catalysis Be as Relevant in Future Biorefineries as in Crude Oil Refineries?, Angew. Chem. Int. Ed, vol.53, pp.8621-8626, 2014.

D. Phan and E. Lee, Catalytic Hydroisomerization Upgrading of Vegetable Oil-Based Insulating Oil. Catalysts, vol.8, p.131, 2018.

C. Bouchy, G. Hastoy, E. Guillon, and J. A. Martens, Fischer-Tropsch Waxes Upgrading via Hydrocracking and Selective Hydroisomerization, Oil Gas Sci. Technol. -Rev. IFP Energies nouvelles, vol.64, pp.91-112, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02001400

J. Weitkamp, Catalytic Hydrocracking-Mechanisms and Versatility of the Process, ChemCatChem, vol.4, pp.292-306, 2012.

J. W. Thybaut, L. C. Narasimhan, G. B. Marin, J. F. Denayer, G. V. Baron et al., Alkylcarbenium Ion Concentrations in Zeolite Pores During Octane Hydrocracking on Pt/H-USY Zeolite, Catal. Lett, vol.94, pp.81-88, 2004.

G. A. Olah, General Concept and Structure of Carbocations Based on Differentiation of Trivalent (Classical) Carbenium Ions from Three-Center Bound Penta-or Tetracoordinated (Nonclassical) Carbonium Ions. The Role of Carbocations in Electrophilic Reactions, J. Am. Chem. Soc, vol.94, pp.808-820, 1972.

D. M. Brouwer and H. Hogeven, Electrophilic Substitutions at Alkanes and in Alkylcarbonium Ions, Prog. Phys. Org. Chem, vol.9, pp.179-240, 1972.

J. B. Nicholas and J. F. Haw, The Prediction of Persistent Carbenium Ions in Zeolites, J. Am. Chem. Soc, vol.120, pp.11804-11805, 1998.

I. I. Ivanova and Y. G. Kolyagin, Impact of in Situ MAS NMR Techniques to the Understanding of the Mechanisms of Zeolite Catalyzed Reactions, Chem. Soc. Rev, vol.39, pp.5018-5050, 2010.

W. Dai, C. Wang, X. Yi, A. Zheng, L. Li et al., Identification of tert-Butyl Cations in Zeolite H-ZSM-5: Evidence from NMR Spectroscopy and DFT Calculations, Angew. Chem. Int. Edit, vol.54, pp.8783-8786, 2015.

M. Huang, Q. Wang, X. Yi, Y. Chu, W. Dai et al., Insight into the Formation of the tert-butyl Cation Confined inside H-ZSM-5 Zeolite from NMR Spectroscopy and DFT Calculations, Chem. Commun, vol.52, pp.10606-10608, 2016.

V. B. Kazansky and I. N. Senchenya, Quantum Chemical Study of the Electronic Structure and Geometry of Surface Alkoxy Groups as Probable Active Intermediates of Heterogeneous Acidic Catalysts. What Are The Adsorbed Carbenium Ions?, J. Catal, vol.119, pp.108-120, 1989.

M. V. Frash, V. B. Kazansky, R. A. Rigby, and R. A. Van-santen, Cracking of Hydrocarbons on Zeolite Catalysts: Density Functional and Hartree?Fock Calculations on the Mechanism of the ?-Scission Reaction, J. Phys. Chem. B, vol.102, pp.2232-2238, 1998.

J. F. Denayer, G. V. Baron, G. Vanbutsele, P. A. Jacobs, and J. A. Martens, Evidence for Alkylcarbenium Ion Reaction Intermediates from Intrinsic Reaction Kinetics of C6-C9 n

, Alkane Hydroisomerization and Hydrocracking on Pt/H-Y and Pt/USY Zeolites, J. Catal, vol.190, pp.469-473, 2000.

M. Boronat, P. M. Viruela, and A. Corma, Reaction Intermediates in Acid Catalysis by Zeolites: Prediction of the Relative Tendency to form Alkoxides or Carbocations as a Function of Hydrocarbon Nature and Active Site Structure, J. Am. Chem. Soc, vol.126, pp.3300-3309, 2004.

F. Leydier, C. Chizallet, D. Costa, and P. Raybaud, Revisiting Carbenium Chemistry on Amorphous Silica-Alumina: Unraveling their Milder Acidity as Compared to Zeolites
URL : https://hal.archives-ouvertes.fr/hal-01176479

, J. Catal, vol.325, pp.35-47, 2015.

J. Rey, P. Raybaud, and C. Chizallet, Ab Initio Simulation of the Acid Sites at the External Surface of Zeolite Beta, vol.9, pp.2176-2185, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01701465

E. Gutierrez-acebo,

J. Rey, C. Bouchy, Y. Schuurman, and C. Chizallet, Location of the Active Sites for Ethylcyclohexane Hydroisomerization by Ring Contraction and Expansion in the EUO Zeolitic Framework, ACS Catal, vol.9, pp.1692-1704, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02076426

C. Tuma and J. Sauer, Protonated Isobutene in Zeolites: tert-butyl Cation or Alkoxide?, Angew. Chem. Int. Edit, vol.44, pp.4769-4771, 2005.

C. Tuma and J. Sauer, Treating Dispersion Effects in Extended Systems by Hybrid MP2:DFT Calculations-Protonation of Isobutene in Zeolite Ferrierite, Phys. Chem. Chem. Phys, vol.8, pp.3955-3965, 2006.

C. Tuma, T. Kerber, and J. Sauer, The tert-butyl Cation in H-Zeolites: Deprotonation to Isobutene and Conversion into Surface Alkoxides, Angew. Chem. Int. Edit, vol.49, pp.4678-4680, 2010.

P. Cnudde, K. Wispelaere, J. De;-van-der-mynsbrugge, M. Waroquier, and V. Van-speybroeck, Effect of Temperature and Branching on the Nature and Stability of Alkene Cracking Intermediates in H-ZSM-5, J. Catal, vol.345, pp.53-69, 2017.

J. Hajek, J. Van-der-mynsbrugge, K. Wispelaere, and . De,

P. Cnudde, L. Vanduyfhuys, M. Waroquier, and V. Van-speybroeck, On the Stability and Nature of Adsorbed Pentene in Brønsted Acid Zeolite H-ZSM-5 at 323K, J. Catal, vol.340, pp.227-235, 2016.

P. Cnudde, K. Wispelaere, L. Vanduyfhuys, R. Demuynck, J. Van-der-mynsbrugge et al., How Chain Length and Branching Influence the Alkene Cracking Reactivity on H-ZSM-5, ACS Catal, vol.8, pp.9579-9595, 2018.

V. Van-speybroeck, K. Hemelsoet, L. Joos, M. Waroquier, R. G. Bell et al.,

A. , Advances in Theory and their Application within the Field of Zeolite Chemistry

, Chem. Soc. Rev, vol.44, pp.7044-7111, 2015.

T. Bu?ko, L. Benco, J. Hafner, and J. G. Ángyán, Monomolecular Cracking of Propane over Acidic Chabazite, J. Catal, vol.279, pp.220-228, 2011.

J. Rey, A. Gomez, P. Raybaud, C. Chizallet, and T. Bu?ko, On the Origin of the Difference Between Type A and Type B Skeletal Isomerization of Alkenes Catalyzed by Zeolites: The Crucial Input of ab initio Molecular Dynamics, J. Catal, vol.373, pp.361-373, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02149821

E. A. Carter, G. Ciccotti, J. T. Hynes, and R. Kapral, Constrained Reaction Coordinate Dynamics for the Simulation of Rare Events, Chem. Phys. Lett, vol.156, pp.472-477, 1989.

G. Ciccotti and M. Sprik, Free Energy from Constrained Molecular Dynamics

, J. Chem. Phys, vol.109, pp.7737-7744, 1998.

J. W. Thybaut, G. B. Marin, G. V. Baron, P. A. Jacobs, and J. A. Martens, Alkene Protonation Enthalpy Determination from Fundamental Kinetic Modeling of Alkane Hydroconversion on Pt/H-(US)Y-Zeolite, J. Catal, vol.202, pp.324-339, 2001.

P. Raybaud, A. Patrigeon, and H. Toulhoat, The Origin of the C7-Hydroconversion Selectivities on Y, ?, ZSM-22, ZSM-23, and EU-1 Zeolites, J. Catal, vol.197, pp.98-112, 2001.

T. Demuth, X. Rozanska, L. Benco, J. Hafner, R. A. Van-santen et al., Catalytic Isomerization of 2-pentene in H-ZSM-22-A DFT Investigation, J. Catal, vol.214, pp.68-77, 2003.

B. Huang, P. Bai, M. Neurock, and R. J. Davis, Conversion of n-Hexane and n-Dodecane over H-ZSM-5, H-Y and Al-MCM-41 at Supercritical Conditions, Appl. Catal. A-Gen, vol.546, pp.149-158, 2017.

M. A. Natal-santiago, R. Alcalá, and J. A. Dumesic, DFT Study of the Isomerization of

, Hexyl Species Involved in the Acid-Catalyzed Conversion of 2-Methyl-Pentene-2, J. Catal, vol.181, pp.124-144, 1999.

G. G. Martens, G. B. Marin, J. A. Martens, P. A. Jacobs, and G. V. Baron, A Fundamental Kinetic Model for Hydrocracking of C8 to C12 Alkanes on Pt/US-Y Zeolites, J. Catal, vol.195, pp.253-267, 2000.

D. M. Brouwer and J. A. Van-doorn, Spectroscopic Observation of a 1,3-Hydrogen Shift in 2,4-Dimethylpentyl Cation, Recl. Trav. Chim. Pays-Bas, vol.88, pp.573-576, 1969.

M. A. Baltanas, K. K. Van-raemdonck, G. F. Froment, and S. R. Mohedas, Fundamental Kinetic Modeling of Hydroisomerization and Hydrocracking on Noble Metal-Loaded Faujasites. 1. Rate Parameters for Hydroisomerization, Ind. Eng. Chem. Res, vol.28, pp.899-910, 1989.

J. Schweitzer, P. Galtier, D. Schweich, and . Single, Events Kinetic Model for the hydrocracking of Paraffins in a Three-Phase Reactor, Chem. Eng. Sci, vol.54, pp.2441-2452, 1999.

G. Kresse and J. Hafner, Ab Initio Molecular Dynamics for Liquid Metals, Phys. Rev. B, vol.47, pp.558-561, 1993.

G. Kresse and J. Hafner, Ab Initio Molecular-Dynamics Simulation of the Liquid-Metal-Amorphous-Semiconductor Transition in Germanium, Phys. Rev. B, vol.49, pp.14251-14269, 1994.

G. Kresse and J. Furthmüller, Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set, Phys. Rev. B, vol.54, pp.11169-11186, 1996.

P. E. Blöchl, Projector Augmented-Wave Method, Phys. Rev. B, vol.50, pp.17953-17979, 1994.

G. Kresse and D. Joubert, From Ultrasoft Pseudopotentials to the Projector Augmented-Wave Method, Phys. Rev. B, vol.59, pp.1758-1775, 1999.

J. P. Perdew, K. Burke, and M. Ernzerhof, Generalized Gradient Approximation Made Simple, Phys. Rev. Lett, vol.77, pp.3865-3868, 1996.

S. Grimme and . Semiempirical, GGA-Type Density Functional Constructed with a Long-Range Dispersion Correction, J. Comput. Chem, vol.27, pp.1787-1799, 2006.

F. Göltl, A. Grüneis, T. Bu?ko, and J. Hafner, Van der Waals Interactions between Hydrocarbon Molecules and Zeolites: Periodic Calculations at Different Levels of Theory, from Density Functional Theory to the Random Phase Approximation and Møller-Plesset Perturbation Theory, J. Chem. Phys, p.114111, 2012.

M. Silaghi, C. Chizallet, E. Petracovschi, T. Kerber, J. Sauer et al., Regioselectivity of Al-O Bond Hydrolysis during Zeolites Dealumination Unified by Brønsted-Evans-Polanyi Relationship, ACS Catal, vol.5, pp.11-15, 2015.

T. Bu?ko, J. Hafner, S. Lebègue, and J. G. Ángyán, Improved Description of the Structure of Molecular and Layered Crystals, J. Phys. Chem. A, vol.114, pp.11814-11824, 2010.

T. Bu?ko, J. Hafner, and J. G. Angyán, Geometry Optimization of Periodic Systems Using Internal Coordinates, J. Chem. Phys, p.124508, 2005.

T. Bu?ko, Transition state optimization of periodic systems using delocalized internal coordinates, Theor. Chem. Acc, vol.137, p.164, 2018.

K. Fukui, Formulation of the Reaction Coordinate, J. Phys. Chem, vol.74, pp.4161-4163, 1970.

K. Fukui, The Path of Chemical Reactions -the IRC Approach, Accounts Chem. Res, vol.14, pp.363-368, 1981.

H. P. Hratchian and H. B. Schlegel, Following Reaction Pathways Using a Damped Classical Trajectory Algorithm, J. Phys. Chem. A, vol.106, pp.165-169, 2002.

D. Frenkel and B. Smit, Understanding Molecular Simulation. From Algorithms to Applications; Computational science series, 2002.

T. Bu?ko, S. Chibani, J. Paul, L. Cantrel, and M. Badawi, Dissociative Iodomethane Adsorption on Ag-MOR and the Formation of AgI clusters: An Ab Initio Molecular Dynamics Study, Phys. Chem. Chem. Phys, vol.19, pp.27530-27543, 2017.

T. Bu?ko, Ab Initio Calculations of Free-Energy Reaction Barriers, J. Phys. Condens. Matter, p.64211, 1920.

T. Bu?ko and J. Hafner, The Role of Spatial Constraints and Entropy in the Adsorption and Transformation of Hydrocarbons catalyzed by zeolites, J. Catal, vol.329, pp.32-48, 2015.

A. Laio and M. Parrinello, Escaping Free-Energy Minima, Proc. Natl. Acad. Sci. U.S.A, vol.99, pp.12562-12566, 2002.

G. Rasul, G. K. Prakash, and G. A. Olah, CCSD(T), and Density Functional Theory Study of the 2-Butyl Cation: New Insight into the Methyl-and Hydrogen-Bridged Structures, J.Phys.Chem. A, vol.119, pp.5762-5769, 2015.

I. V. Vr?ek, V. Vr?ek, and H. Siehl, Quantum Chemical Study of Degenerate Hydride Shifts in Acyclic Tertiary Carbocations, J. Phys. Chem. A, vol.106, pp.1604-1611, 2002.

G. A. Olah, G. K. Prakash, and G. Rasul, Ab Initio/GIAO-CCSD(T) 13 C NMR Study of the Rearrangement and Dynamic Aspects of Rapidly Equilibrating Tertiary Carbocations, C 6 H 13 + and C 7 H 15 +, J. Comput. Chem, vol.37, pp.70-77, 2016.

C. J. Collins, Protonated Cyclopropanes, Chem. Rev, vol.69, pp.543-550, 1969.

G. J. Karabatsos and C. E. Orzech, Carbonium Ion Rearrangements. V.11,3-Hydride Shifts in the 1-Propyl Cation, J. Am. Chem. Soc, vol.84, pp.2838-2839, 1962.

C. C. Lee and L. Gruber, Protonated Cyclopropanes. II. The Solvolysis of Cyclopropane in Tritiated Sulfuric Acid, J. Am. Chem. Soc, vol.90, pp.3775-3778, 1968.

G. Piccini, M. Alessio, and J. Sauer, Ab Initio Calculation of Rate Constants for Molecule-Surface Reactions with Chemical Accuracy, Angew. Chem. Int. Edit, vol.55, pp.5235-5237, 2016.

M. Rybicki and J. Sauer, Ab Initio Prediction of Proton Exchange Barriers for Alkanes at Brønsted Sites of Zeolite H-MFI, J. Am. Chem. Soc, vol.140, pp.18151-18161, 2018.

P. N. Plessow and F. Studt, Olefin Methylation and Cracking Reactions in H-SSZ-13

, Investigated with ab initio and DFT Calculations, Catal. Sci. Technol, vol.8, pp.4420-4429, 2018.

T. J. Goncalves, P. N. Plessow, and F. Studt, On the Accuracy of Density Functional Theory in Zeolite Catalysis, ChemCatChem, 2019.

D. Rocca, A. Dixit, M. Badawi, S. Lebègue, T. Gould et al., Bridging Molecular Dynamics and Correlated Wave-Function Methods for Accurate Finite-Temperature Properties, Phys. Rev. Materials, vol.3, p.40801, 2019.

W. F. Wynne-jones and H. Eyring, The Absolute Rate of Reactions in Condensed Phases, J. Chem. Phys, vol.3, pp.492-502, 1935.

L. P. Oliveira, D. De;-hudebine, D. Guillaume, J. J. Verstraete, and J. F. Joly, A Review of Kinetic Modeling Methodologies for Complex Processes, Oil Gas Sci. Technol. -Rev. IFP Energies nouvelles, vol.71, p.45, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01395195

P. S. Mendes, J. M. Silva, M. F. Ribeiro, P. Duchêne, A. Daudin et al., Quantification of metal-acid balance in hydroisomerization catalysts: A step further toward catalyst design, AIChE J, vol.63, pp.2864-2875, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01581867

K. Surla, D. Guillaume, J. J. Verstraete, and P. Galtier, Kinetic Modeling using the Single-Event Methodology, Oil Gas Sci. Technol. -Rev. IFP Energies nouvelles, vol.66, pp.343-365, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01937403

B. D. Vandegehuchte, J. W. Thybaut, and G. B. Marin, Unraveling Diffusion and Other Shape Selectivity Effects in ZSM5 Using n -Hexane Hydroconversion Single-Event Microkinetics, Ind. Eng. Chem. Res, vol.53, pp.15333-15347, 2014.

E. Valéry, D. Guillaume, K. Surla, P. Galtier, J. Verstraete et al., Kinetic Modeling of Acid Catalyzed Hydrocracking of Heavy Molecules, Ind. Eng. Chem. Res, vol.46, pp.4755-4763, 2007.