V. Van Speybroeck

Normal mode analysis of macromolecular systems with the mobile block Hessian method

A. Ghysels, V. Van Speybroeck, D. Van Neck, B.R. Brooks, M. Waroquier
AIP Conference Proceedings
1642 (2015), 559
2015
P1

Abstract 

Until recently, normal mode analysis (NMA) was limited to small proteins, not only because the required energy minimization is a computationally exhausting task, but also because NMA requires the expensive diagonalization of a 3N(a) x 3N(a) matrix with N-a the number of atoms. A series of simplified models has been proposed, in particular the Rotation-Translation Blocks (RTB) method by Tama et al. for the simulation of proteins. It makes use of the concept that a peptide chain or protein can be seen as a subsequent set of rigid components, i.e. the peptide units. A peptide chain is thus divided into rigid blocks with six degrees of freedom each.

Recently we developed the Mobile Block Hessian (MBH) method, which in a sense has similar features as the RTB method. The main difference is that MBH was developed to deal with partially optimized systems. The position/orientation of each block is optimized while the internal geometry is kept fixed at a plausible - but not necessarily optimized - geometry. This reduces the computational cost of the energy minimization. Applying the standard NMA on a partially optimized structure however results in spurious imaginary frequencies and unwanted coordinate dependence. The MBH avoids these unphysical effects by taking into account energy gradient corrections. Moreover the number of variables is reduced, which facilitates the diagonalization of the Hessian.

In the original implementation of MBH, atoms could only be part of one rigid block. The MBH is now extended to the case where atoms can be part of two or more blocks. Two basic linkages can be realized: (1) blocks connected by one link atom, or (2) by two link atoms, where the latter is referred to as the hinge type connection. In this work we present the MBH concept and illustrate its performance with the crambin protein as an example.

Insight into the Effect of Water on the Methanol-to-Olefins Conversion in H-SAPO-34 from Molecular Simulations and in Situ Microspectroscopy

K. De Wispelaere, C.S. Wondergem, B. Ensing, K. Hemelsoet, E.J. Meijer, B.M. Weckhuysen, V. Van Speybroeck, J. Ruiz-Martinez
ACS Catalysis
6, 1991-2002
2016
A1

Abstract 

The role of water in the methanol-to-olefins (MTO) process over H-SAPO-34 has been elucidated by a combined theoretical and experimental approach, encompassing advanced molecular dynamics simulations and in-situ micro-spectroscopy. First principle calculations at the molecular level point out that water competes with methanol and propene for direct access to the Brønsted acid sites. This results in less efficient activation of these molecules, which are crucial for the formation of the hydrocarbon pool. Furthermore, lower intrinsic methanol reactivity towards methoxide formation has been observed. These observations are in line with a longer induction period observed from in-situ UV-Vis micro-spectroscopy experiments. These experiments revealed a slower and more homogeneous discoloration of H-SAPO-34, while in-situ confocal fluorescence microscopy confirmed the more homogeneous distribution and larger amount of MTO intermediates when co-feeding water. As such it is show that water induces a more efficient use of the H-SAPO-34 catalyst crystals at the microscopic level. The combined experimental theoretical approach gives a profound insight into the role of water on the catalytic process at the molecular and single particle level.

The enantioselectivity of the manganese-salen complex in the epoxidation of unfunctionalized olefins and the influence of grafting

T. Bogaerts, S. Wouters, P. Van der Voort, V. Van Speybroeck
Journal of Molecular Catalysis A: Chemical
Vol. 406, 106-113
2015
A1

Abstract 

Jacobsen’s complexes are famous for their usability for enantioselective epoxidations. However, the applicability of this catalytic system has been severely limited by several practical problems such as deactivation and separation after reaction. Grafting of Jacobsen-type complexes on solid supports is an attractive way to overcome these problems but led to a decrease in selectivity. A combined theoretical and experimental approach is presented to unravel the factors governing enantioselectivity. The importance of different substituents was determined by analyzing the transition state for the oxygen transfer using the full system as a model. An analysis of the asymmetric complex has shown an inherent tendency for a decreased selectivity due to the lack of specific bulky groups. Experimentally an immobilized Jacobsen catalyst on a metal organic framework (MIL-101) was synthesized which confirms the computational tendencies but the decrease in selectivity is limited, indicating that the MIL-101(Cr) is a suitable carrier for this complex.

Open Access version available at UGent repository

DOI 

10.1016/j.molcata.2015.05.020

Mechanistic investigation on the oxygen transfer with the manganese-salen complex

T. Bogaerts, S. Wouters, P. Van der Voort, V. Van Speybroeck
ChemCatChem
7 (17), 2711–2719
2015
A1

Abstract 

The most well-known application of salen complexes is the use of a chiral ligand loaded with manganese to form the Jacobsen complex. This organometallic catalyst is used in the epoxidation of unfunctionalized olefins and can achieve very high selectivities. Although this application was proposed many years ago, the mechanism of oxygen transfer remains a question until now. In this paper, the epoxidation mechanism is investigated by an ab initio kinetic modeling study. First of all a proper DFT functional is selected which yields the correct ordering of the various spin states. Our results show that the epoxidation proceeds via a radical intermediate. Starting from the radical intermediate, these results can explain the experiments with radical probes. The subtle influences in the transition state using the full Jacobsen catalyst explain the experimentally observed product distribution.

On the stability and nature of adsorbed pentene in Brønsted acid zeolite H-ZSM-5 at 323 K

J. Hajek, J. Van der Mynsbrugge, K. De Wispelaere, P. Cnudde, L. Vanduyfhuys, M. Waroquier, V. Van Speybroeck
Journal of Catalysis
340, 227 - 235
2016
A1

Abstract 

Adsorption of linear pentenes in H-ZSM-5 at 323 K is investigated using contemporary static and molecular dynamics methods. A physisorbed complex corresponding to free pentene, a π-complex and a chemisorbed species may occur. The chemisorbed species can be either a covalently bonded alkoxide or an ion pair, the so-called carbenium ion. Without finite temperature effects, the π-complex is systematically slightly more bound than the chemisorbed alkoxide complex, whereas molecular dynamics calculations at 323 K yield an almost equal stability of both species. The carbenium ion was not observed during simulations at 323 K. The transformation from the π-complex to the chemisorbed complex is activated by a free energy in the range of 33–42 kJ/mol. Our observations yield unprecedented insights into the stability of elusive intermediates in zeolite catalysis, for which experimental data are very hard to measure.

Open Access version available at UGent repository

PPV Polymerization via the Gilch Route: Diradical Character of Monomers

J.D. Nikolic, S. Wouters, J. Romanova, A. Shimizu, B. Champagne, T. Junkers, D. Vanderzande, D. Van Neck, M. Waroquier, V. Van Speybroeck, S. Catak
Chemistry - A European Journal
21, 19176-19185
2015
A1

Abstract 

Despite various studies on the polymerization of poly(p-phenylene vinylene) (PPV) through different precursor routes, detailed mechanistic knowledge on the individual reaction steps and intermediates is still incomplete. The present study aims to gain more insight into the radical polymerization of PPV through the Gilch route. The initial steps of the polymerization involve the formation of a p-quinodimethane intermediate, which spontaneously self-initiates through a dimerization process leading to the formation of diradical species; chain propagation ensues on both sides of the diradical or chain termination occurs by the formation of side products, such as [2.2]paracyclophanes. Furthermore, different p-quinodimethane systems were assessed with respect to the size of their aromatic core as well as the presence of heteroatoms in/on the conjugated system. The nature of the aromatic core and the specific substituents alter the electronic structure of the p-quinodimethane monomers, affecting the mechanism of polymerization. The diradical character of the monomers has been investigated with several advanced methodologies, such as spin-projected UHF, CASSCF, CASPT2, and DMRG calculations. It was shown that larger aromatic cores led to a higher diradical character in the monomers, which in turn is proposed to cause rapid initiation.

Carbon Capture Turned Upside Down: High-Temperature Adsorption & Low-Temperature Desorption (HALD)

L. Joos, K. Lejaeghere, J. Huck, V. Van Speybroeck, B. Smit
Energy & Environmental Science
8, 2480-2491
2015
A1

Abstract 

Carbon Capture & Sequestration (CCS) could reduce CO2 emissions from large fossil-fuel power plants in the short term, but the high energy penalty of the process hinders its industrial deployment. Moreover, the utility of nanoporous materials, known to be selective for the CO2/N2 separation, is drastically reduced due to the competitive adsorption with H2O. Taking advantage of the power plant's waste heat to perform CCS while at the same time surmounting the negative effect of H2O is therefore an attractive idea. We propose an upside-down approach for CCS in nanoporous materials, High-temperature Adsorption & Low-temperature Desorption (HALD), that exploits the temperature-dependent competitive adsorption of CO2 and H2O. First, we provide a theoretical background for this entropy-driven behavior and demonstrate under what conditions competitive adsorption can be in favor of CO2 at high temperature and in favor of H2O at low temperature. Then, molecular simulations in all-silica MFI provide a proof of concept. The International Zeolite Association database is subsequently screened for potential candidates and finally, the most promising materials are selected using a post-Pareto search algorithm. The proposed post-Pareto approach is able to select the material that shows an optimal combination of multiple criteria, such as CO2/H2O selectivity, CO2/N2 selectivity, CO2 uptake and H2O uptake. As a conclusion, this work provides new perspectives to reduce the energy requirement for CCS and to overcome the competitive adsorption of H2O.

Open Access version available at UGent repository

Synthesis of poly(2-oxazoline)s with side chain methyl ester functionalities: Detailed understanding of copolymerization behavior of methyl ester containing monomers with 2-alkyl-2-oxazolines

P. Bouten, D. Hertsen, M. Vergaelen, B. Monnery, S. Catak, J. van Hest, V. Van Speybroeck, R. Hoogenboom
Polymer Chemistry
7 (17), 2711-2719
2015
A1

Abstract 

Poly(2-oxazoline)s with methyl ester functionalized side chains are interesting as they can undergo a direct amidation reaction or can be hydrolyzed to the carboxylic acid, making them versatile functional polymers for conjugation. In this work, detailed studies on the homo- and copolymerization kinetics of two methyl ester functionalized 2-oxazoline monomers with 2-methyl-2-oxazoline, 2-ethyl-2-oxazoline, and 2-n-propyl-2-oxazoline are reported. The homopolymerization of the methyl ester functionalized monomers is found to be faster compared to the alkyl monomers, while copolymerization unexpectedly reveals that the methyl ester containing monomers significantly accelerate the polymerization. A computational study confirms that methyl ester groups increase the electrophilicity of the living chain end, even if they are not directly attached to the terminal residue. Moreover, the electrophilicity of the living chain end is found to be more important than the nucleophilicity of the monomer in determining the rate of propagation. However, the monomer nucleophilicity can be correlated with the different rates of incorporation when two monomers compete for the same chain end, that is, in copolymerizations. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015

Beyond the diketopiperazine family with alternatively bridged brevianamide F analogues

I. Wauters, H. Goossens, E. Delbeke, K. Muylaert, B.I. Roman, K. Van Hecke, V. Van Speybroeck, C.V. Stevens
Chemistry - A European Journal
80 (16), 8046-8054
2015
A1

Abstract 

A method for the preparation of 3,5-bridged piperazin-2-ones from a tryptophan–proline-based diketopiperazine is described using diphosgene to induce the ring closure. Density functional theory calculations were conducted to study the mechanism of this C–C bond formation. Several derivatives of the thus obtained α-chloroamine were synthesized by substitution of the chlorine atom using a range of O-, N-, S-, and C-nucleophiles. This novel class of brevianamide F analogues possess interesting breast cancer resistance protein inhibitory activity.

On the convergence of atomic charges with the size of the enzymatic environment

D.E.P. Vanpoucke, J. Olah, F. De Proft, V. Van Speybroeck, G. Roos
Journal of Chemical Information and Modeling (JCIM)
Volume 55 Issue 3 page 564–571
2015
A1

Abstract 

Atomic charges are a key concept to give more insight into the electronic structure and chemical reactivity. The Hirshfeld-I partitioning scheme applied to the model protein human 2-cysteine peroxiredoxin thioredoxin peroxidase B is used to investigate how large a protein fragment needs to be in order to achieve convergence of the atomic charge of both, neutral and negatively charged residues. Convergence in atomic charges is rapidly reached for neutral residues, but not for negatively charged ones. This study pinpoints difficulties on the road towards accurate modeling of negatively charged residues of large biomolecular systems in a multiscale approach.

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