Center for Molecular Modeling - IAP VI P6/27

Critical analysis of the accuracy of models predicting or extracting liquid structure information

michel — Tue, 26 Nov 2013 20:34:03 +0000

M. Van Houteghem, A. Ghysels, T. Verstraelen, W. Poelmans, M. Waroquier, V. Van Speybroeck

Journal of Physical Chemistry B

118 (9), 2451–2470

2014

Abstract

This work aims at a critical assessment of properties predicting or extracting information on the density and structure of liquids. State-of-the-art NVT and NpT molecular dynamics (MD) simulations have been performed on five liquids: methanol, chloroform, acetonitrile, tetrahydrofuran and ethanol. These simulations allow the computation of properties based on first principles, including the equilibrium density and radial distribution functions (RDFs), characterizing the liquid structure. Refinements have been incorporated in the MD simulations by taking into account Basis Set Superposition Errors (BSSE). An extended BSSE model for an instantaneous evaluation of the BSSE corrections has been proposed, and their impact on the liquid properties has been assessed. If available, the theoretical RDFs have been compared with the experimentally derived RDFs. For some liquids significant discrepancies have been observed and a profound but critical investigation is presented to unravel the origin of these deficiencies. This discussion is focused on tetrahydrofuran where the experiment reveals some prominent peaks completely missing in any MD simulation. Experiments providing information on liquid structure consist mainly of neutron diffraction measurements offering total structure factors as the primary observables. The splitting of these factors in reciprocal space into intra- and intermolecular contributions is extensively discussed, together with their sensitivity in reproducing correct RDFs in coordinate space.

DOI

http://dx.doi.org/10.1021/jp411737s

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Bimetallic–Organic Framework as a Zero-Leaching Catalyst in the Aerobic Oxidation of Cyclohexene

bogaerts — Tue, 09 Jul 2013 09:09:00 +0000

Y-Y Liu, K. Leus, T. Bogaerts, K. Hemelsoet, E. Bruneel, V. Van Speybroeck, P. Van der Voort

ChemCatChem

5 (12), 3657–3664

2013

Abstract

A gallium 2,2′-bipyridine-5,5′-dicarboxylate metal–organic framework (MOF), denoted as COMOC-4, has been synthesized by solvothermal synthesis. This MOF exhibits the same topology as MOF-253. CuCl₂ was incorporated into COMOC-4 by a post-synthetic modification (PSM). The spectroscopic absorption properties of the MOF framework before and after PSM were compared with theoretical data obtained by employing molecular dynamics combined with time-dependent DFT calculations on both the as-synthesized and functionalized linker. The catalytic behavior of the resulting Cu²⁺@COMOC-4 material was evaluated in the aerobic oxidation of cyclohexene with isobutyraldehyde as a co-oxidant. In addition, the catalytic performance of Cu²⁺@COMOC-4 was compared with that of the commercially available Cu-BTC (BTC=benzene-1,3,5-tricarboxylate) MOF. Cu²⁺@COMOC-4 exhibits a good cyclohexene conversion and an excellent selectivity towards cyclohexene oxide in comparison to the Cu-based reference catalyst. Furthermore, no leaching of the active Cu sites was observed during at least four consecutive runs.

DOI

http://dx.doi.org/10.1002/cctc.201300529

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manuscript.pdf

Insight in the activity and diastereoselectivity of various Lewis acid catalysts for the citronellal cyclization

mat — Wed, 13 Feb 2013 12:38:41 +0000

M. Vandichel, F. Vermoortele, S. Cottenie, D. De Vos, M. Waroquier, V. Van Speybroeck

Journal of Catalysis

305, 118-129

2013

Abstract

Industrial (-)-menthol production generally relies on the hydrogenation of (-)-isopulegol, which is in turn produced with high selectivity by cyclization of (+)-citronellal. This paper uses a combined theoretical and experimental approach to study the activity and selectivity of three Lewis acid catalysts for this reaction, namely ZnBr2, aluminum tris(2,6-diphenylphenoxide) (ATPH) and the heterogeneous metal-organic framework Cu3BTC2 (BTC = benzene-1,3,5-tricarboxylate). ATPH is a strong Lewis acid homogeneous catalyst with bulky ligands which provides very high selectivities for the desired stereo-isomer (> 99 %). The performance of the catalysts was evaluated as a function of temperature, which revealed that higher catalyst activity allows working at lower temperatures and improves the selectivity for isopulegol. The selectivity distribution is kinetically driven for ZnBr2 and ATPH. The theoretical selectivity distributions rely on the determination of an extensive set of diastereomeric transition states, for which the differences in free energy have been calculated using a complementary set of ab initio techniques. Given the sensitivity of the selectivity to small Gibbs free energy differences, the agreement between experimental and theoretical selectivities is satisfactory. On basis of the obtained insights rational design of new catalysts may be obtained. As proof of concept, the hypothetical Cu3(BTC-(NO2)3)2 Lewis catalyst – in which each phenyl hydrogen of the BTC ligand is replaced by a nitro group - is predicted to be very selective.

Open Access version available at UGent repository

DOI

http://dx.doi.org/10.1016/j.jcat.2013.04.017

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Origins of the Solvent Effect on the Propagation Kinetics of Acrylic Acid and Methacrylic Acid

michel — Wed, 15 Aug 2012 04:50:02 +0000

I. Değirmenci, T. Furuncuoğlu, O. Karahan, V. Van Speybroeck, M. Waroquier, V. Aviyente

Journal of Polymer Science Part A: Polymer Chemistry

51 (9), 2024–2034

2013

Abstract

In this study, the relative rate of polymerization of acrylic acid (AA) versus methacrylic acid (MAA) and the effect of water on the polymerization kinetics are investigated within a combined static and molecular dynamics set of computational tools. Experimentally the relative rate of propagation of AA versus MAA is around 35 in bulk and 31 in water. Classical Molecular Dynamics calculations have been carried out to determine the location of the solvent molecules in the proximity of the dimeric poly(AA) and poly(MAA) units. A combined implicit/explicit solvent model was used for the evaluation of the kinetics of the dimeric polymer chains. We show that the rate acceleration of both polymers in water is mainly due to entropic rather than electrostatic effects and is in agreement with experimental findings. Moreover the slower propagation rate of MAA versus AA is ascribed to additional steric effects present in MAA due to the methyl group at the α position of the monomer. Among the functionals used, the M06-2X/6-311+G(3df,2p)//B3LYP/6-31+G(d) methodology reproduces the experimental rate constants quantitatively the best. © 2013 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2013

DOI

http://dx.doi.org/10.1002/pola.26589

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Ti-functionalized NH2-MIL-47: an effective and stable epoxidation catalyst

wim — Tue, 07 Aug 2012 11:18:13 +0000

K. Leus, G. Vanhaelewyn, T. Bogaerts, Y-Y Liu, F. Esquivel, F. Callens, G.B. Marin, V. Van Speybroeck, H. Vrielinck, P. Van der Voort

Catalysis Today

208, 97-105

2013

Abstract

In this paper, we describe the post-functionalization of a V-containing Metal-organic framework with TiO(acac)2 to create a bimetallic oxidation catalyst. The catalytic performance of this V/Ti-MOF was examined for the oxidation of cyclohexene using molecular oxygen as oxidant in combination with cyclohexanecarboxaldehyde as co-oxidant. A significantly higher cyclohexene conversion was observed for the bimetallic catalyst compared to the non-functionalized material. Moreover, the catalyst could be recycled at least 3 times without loss of activity and stability. No detectable leaching of V or Ti was noted. Electron paramagnetic resonance measurements were performed to monitor the fraction of V-ions in the catalyst in the +IV valence state. A reduction of this fraction by ∼17% after oxidation catalysis is observed, in agreement with the generally accepted mechanism for this type of reaction.

DOI

http://dx.doi.org/10.1016/j.cattod.2012.09.037

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The Conformational Sensitivity of Iterative Stockholder Partitioning Schemes

michel — Wed, 11 Jul 2012 20:29:38 +0000

T. Verstraelen, P.W. Ayers, V. Van Speybroeck, M. Waroquier

Chemical Physics Letters

545, 138-143

2012

Abstract

Chemical interpretation and empirical modeling of partial charges requires a robust partitioning scheme to derive these charges from the molecular electronic density. The degree of undesirable conformational sensitivity is assessed for three iterative stockholder partitioning schemes: Hirshfeld-I (HI), Iterative Stockholder Analysis (ISA) and a new Gaussian ISA variant (GISA). GISA has fewer degrees of freedom than ISA and enforces monotonically decaying pro-atoms. These improvements accelerate the converge of GISA as compared to ISA. However, the conformational sensitivity of the charges does not decrease and is still large compared to HI.

Open Access version available at UGent repository

DOI

http://dx.doi.org/10.1016/j.cplett.2012.07.028

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12 chem phys lett 545,138 Verstraelen.pdf

Analysis of the basis set superposition error in molecular dynamics of hydrogen-bonded liquids: application to methanol

michel — Fri, 15 Jun 2012 19:05:57 +0000

M. Van Houteghem, T. Verstraelen, A. Ghysels, L. Vanduyfhuys, M. Waroquier, V. Van Speybroeck

Journal of Chemical Physics

137 (10), 104506

2012

Abstract

An ecient protocol is presented to compensate for the basis set superposition error (BSSE) in DFT molecular dynamics (MD) simulations using localized Gaussian basis sets. We propose a classical correction term that can be added a posteriori to account for BSSE. It is tested to what extension this term will improve radial distribution functions (RDFs). The proposed term is pairwise between certain atoms in dierent molecules and was calibrated by tting reference BSSE data points computed with the counterpoise method. It is veried that the proposed exponential decaying functional form of the model is valid. This work focuses on hydrogen-bonded liquids, i.e. methanol, and more specic on the intermolecular hydrogen bond, but in principle the method is generally applicable on any type of interaction where BSSE is significant. We evaluated the relative importance of the Grimme-dispersion versus BSSE and found that they are of the same order of magnitude, but with an opposite sign. Upon introduction of the correction, the relevant RDFs, obtained from MD, have amplitudes equal to experiment.

Open Access version available at UGent repository

DOI

http://dx.doi.org/10.1063/1.4749929

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New V-IV-Based Metal-Organic Framework Having Framework Flexibility and High CO2 Adsorption Capacity

mat — Thu, 22 Mar 2012 08:43:25 +0000

Y-Y Liu, S. Couck, M. Vandichel, M. Grzywa, K. Leus, S. Biswas, D. Volkmer, J. Gascon, F. Kapteijn, J.F.M. Denayer, M. Waroquier, V. Van Speybroeck, P. Van der Voort

Inorganic Chemistry

52 (1), 113-120

2013

Abstract

A vanadium based metal–organic framework (MOF), VO(BPDC) (BPDC2– = biphenyl-4,4′-dicarboxylate), adopting an expanded MIL-47 structure type, has been synthesized via solvothermal and microwave methods. Its structural and gas/vapor sorption properties have been studied. This compound displays a distinct breathing effect toward certain adsorptives at workable temperatures. The sorption isotherms of CO2 and CH4 indicate a different sorption behavior at specific temperatures. In situ synchrotron X-ray powder diffraction measurements and molecular simulations have been utilized to characterize the structural transition. The experimental measurements clearly suggest the existence of both narrow pore and large pore forms. A free energy profile along the pore angle was computationally determined for the empty host framework. Apart from a regular large pore and a regular narrow pore form, an overstretched narrow pore form has also been found. Additionally, a variety of spectroscopic techniques combined with N2 adsorption/desorption isotherms measured at 77 K demonstrate that the existence of the mixed oxidation states VIII/VIV in the titled MOF structure compared to pure VIV increases the difficulty in triggering the flexibility of the framework.

DOI

http://dx.doi.org/10.1021/ic301338a

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Synthesis, characterization and sorption properties of NH2-MIL-47

mat — Thu, 22 Mar 2012 08:36:33 +0000

K. Leus, S. Couck, M. Vandichel, G. Vanhaelewyn, Y-Y Liu, G.B. Marin, I. Van Driessche, D. Depla, M. Waroquier, V. Van Speybroeck, J.F.M. Denayer, P. Van der Voort

Physical Chemistry Chemical Physics (PCCP)

14, 15562–15570

2012

Abstract

An amino functionalized vanadium-containing Metal Organic Framework, NH₂-MIL-47 has been synthesized by a hydrothermal reaction in an autoclave. Alternatively, a synthesis route via microwave enhanced irradiation has been optimized to accelerate the synthesis. The NH₂-MIL-47 exhibits the same topology as MIL-47, in which the V center is octahedrally coordinated. After an exchange procedure in DMF the V+III center is oxidized to V+IV, which is confirmed by EPR and XPS measurements. The CO² and CH₄ adsorption properties have been evaluated and compared to MIL-47, showing that both MOFs have an almost similar adsorption capacity and affinity for CO². DFT- based molecular modeling calculations were performed to obtain more insight into the adsorption positions for CO² in NH₂-MIL-47. Furthermore our calculated adsorption enthalpies agree well with the experimental values.

DOI

http://dx.doi.org/10.1039/C2CP42137B

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12 pccp 14,15562 Leus.pdf

Ab initio parametrized force field for the flexible metal-organic framework MIL-53(Al)

michel — Thu, 01 Mar 2012 20:13:18 +0000

L. Vanduyfhuys, T. Verstraelen, M. Vandichel, M. Waroquier, V. Van Speybroeck

Journal of Chemical Theory and Computation (JCTC)

8 (9), 3217-3231

2012

Abstract

A force field is proposed for the flexible metal-organic framework MIL-53(Al), which is calibrated using density functional theory calculations on non-periodic clusters. The force field has three main contributions: an electrostatic term based on atomic charges derived with a modified Hirshfeld-I method, a van der Waals (vdW) term with parameters taken from the MM3 model and a valence force field whose parameters were estimated with a new methodology that uses the gradients and Hessian matrix elements retrieved from non-periodic cluster calculations. The new force field, predicts geometries and cell parameters that compare well with the experimental values both for the large and narrow pore phases. The energy profile along the breathing mode of the empty material reveals the existence of two minima, which confirms the intrinsic bistable behaviour of the MIL-53. Even without the stimulus of external guest molecules the material may transform from the large pore (lp) to the narrow pore (np) phase [Liu et al. JACS 2008, 120, 11813]. The relative stability of the two phases critically depends on the vdW parameters and MM3 dispersion interaction has the tendency to overstabilize the np phase.

DOI

http://dx.doi.org/10.1021/ct300172m

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12 j chem theory comp 8(9)3217 Vanduyfhuys.pdf