Center for Molecular Modeling - ESA

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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14_j_phys_chem_b_118(9)2451_VanHouteghem.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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12 J. Chem. Phys. 137 104506 VanHouteghem.pdf

12 J. Chem. Phys. draft VanHouteghem.pdf

29Si NMR and UV-Raman Investigation of Initial Oligomerization Reaction Pathways in Acid-Catalyzed Silica Sol-Gel Chemistry

wim — Tue, 23 Aug 2011 06:59:51 +0000

A. Depla, D. Lesthaeghe, T.S. van Erp, A. Aerts, K. Houthoofd, F. Fan, C. Li, V. Van Speybroeck, M. Waroquier, C. Kirschhock, J.A. Martens

Journal of Physical Chemistry C

115 (9), 3562–3571

2011

Abstract

The initial molecular steps of the acid-catalyzed silica sol−gel process de-parting from tetraethylorthosilicate (TEOS) were investigated by in situ 29Si NMR and UV−Raman spectroscopy. The use of a substoichiometric H2O:TEOS molar ratio (r-value 0.2−1.2) slowed the silicate oligomerization reaction and allowed unraveling the initial steps of silica condensation. Molecular modeling confirmed Raman signal and 29Si NMR shift assignment. A comprehensive listing of all Raman and 29Si NMR assignments is provided, including unique Raman assignments of cyclosilicates and the linear tetramer. The combination of experiment and modeling allowed an analysis of the reaction kinetics. The derived kinetic model and the experimental observation both revealed that the H2O:TEOS molar ratio had a strong influence on the reaction kinetics but not on the reaction pathways. The multianalytical approach led to development of an oligomerization scheme. As dominant oligomerizations, chain growth, cyclodimerization, and branching were identified. Under the investigated conditions, chains did not grow longer than pentamer, and ring sizes were limited to 6-rings. Chains of 4 Si atoms and 4-rings were abundant species. Branched rings and chains were formed by attachment of dimers and trimers. Gelation proceeded from branched 4-rings and branched chains with limited hydroxyl functionalities.

DOI

http://dx.doi.org/10.1021/jp109901v

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11 j. phys. chem. C 115, 3562 depla.pdf

Atomic Velocity Projection Method: A New Analysis Method for Vibrational Spectra in Terms of Internal Coordinates for a Better Understanding of Zeolite Nanogrowth

wim — Mon, 22 Aug 2011 14:30:27 +0000

M. Van Houteghem, T. Verstraelen, D. Van Neck, C. Kirschhock, J.A. Martens, M. Waroquier, V. Van Speybroeck

Journal of Chemical Theory and Computation (JCTC)

7, 1045-1061

2011

Abstract

An efficient protocol is presented to identify signals in vibrational spectra of silica oligomers based on theoretical molecular dynamics (MD) simulations. The method is based on the projection of the atomic velocity vectors on the tangential directions of the trajectories belonging to a predefined set of internal coordinates. In this way only contributions of atomic motions along these internal coordinates are taken into consideration. The new methodology is applied to the spectra of oligomers and rings, which play an important role in zeolite synthesis. A suitable selection of the relevant internal coordinates makes the protocol very efficient but relies on intuition and theoretical insight. The simulation data necessary to compute vibrational spectra of relevant silica species are obtained through MD using proper force fields. The new methodology—the so-called velocity projection method—makes a detailed analysis of vibrational spectra possible by establishing a one-to-one correspondence between a spectral signal and a proper internal coordinate. It offers valuable perspectives in understanding the elementary steps in silica organization during zeolite nanogrowth. The so-called velocity projection method is generally applicable on data obtained from all types of MD and is a highly valuable alternative to normal-mode analysis which has its limitations due to the presence of many local minima on the potential energy surface. In this work the method is exclusively applied to inelastic neutron scattering, but extension to the infrared power spectrum is apparent.

DOI

http://dx.doi.org/10.1021/ct100538c

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11 j chem theory comp 7, 1045 van houteghem.pdf

Catalytic and molecular separation properties of Zeogrids and Zeotiles

wim — Mon, 22 Aug 2011 14:08:06 +0000

J.A. Martens, J.W. Thybaut, J.F.M. Denayer, S. Pulinthanathu Sree, A. Aerts, M-F. Reyniers, V. Van Speybroeck, M. Waroquier, A. Buekenhoudt, I. Vankelecom, W. Buijs, J. Persoons, G.V. Baron, S. Bals, G. Van Tendeloo, G.B. Marin, P.A. Jacobs, C. Kirschhock

Catalysis Today

168, 17-27

2011

Abstract

Zeogrids and Zeotiles are hierarchical materials built from assembled MFI zeolite precursor units. Permanent secondary porosity in these materials is obtained through self assembly of nanoparticles encountered in MFI zeolite synthesis in the presence of supramolecular templates. Hereon, the aggregated species are termed nanoslabs. Zeogrids are layered materials with lateral spacings between nanoslabs creating galleries qualifying as supermicropores. Zeotiles present a diversity of tridimensional nanoslab assemblies with mesopores. Zeotile-1, -4 and -6 are hexagonal mesostructures. Zeotile-1 has triangular and hexagonal channels; Zeotile-4 has hexagonal channels interconnected via slits. Zeotile-2 has a cubic structure with gyroid type mesoporosity. The behavior of Zeogrids and Zeotiles in adsorption, membrane and chromatographic separation and catalysis has been characterized and compared with zeolites and mesoporous materials derived from unstructured silica sources. Shape selectivity was detected via adsorption of n- and iso-alkanes. The mesoporosity of Zeotiles can be exploited in chromatographic separation of biomolecules. Zeotiles present attractive separation properties relevant to CO2 sequestration. Because of its facile synthesis procedure without hydrothermal steps Zeogrid is convenient for membrane synthesis. The performance of Zeogrid membrane in gas separation, nanofiltration and pervaporation is reported. In the Beckmann rearrangement of cyclohexanone oxime Zeogrids and Zeotiles display a catalytic activity characteristic of silicalite-1 zeolites. Introduction of acidity and redox catalytic activity can be achieved via incorporation of Al and Ti atoms in the nanoslabs during synthesis. Zeogrids are active in hydrocracking, catalytic cracking, alkylation and epoxidation reactions. Zeogrids and Zeotiles often behave differently from ordered mesoporous materials as well as from zeolites and present a valuable extension of the family of hierarchical silicate based materials.

DOI

http://dx.doi.org/10.1016/j.cattod.2011.01.036

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11 cat today 168,17 martens.pdf

UV-Raman and 29Si NMR Spectroscopy Investigation of the Nature of Silicate Oligomers Formed by Acid Catalyzed Hydrolysis and Polycondensation of Tetramethylorthosilicate

wim — Mon, 22 Aug 2011 13:53:23 +0000

A. Depla, E. Verheyen, A. Verfeyken, M. Van Houteghem, K. Houthoofd, V. Van Speybroeck, M. Waroquier, C. Kirschhock, J.A. Martens

Journal of Physical Chemistry C

115(22), 11077-11088

2011

Abstract

Tetramethylorthosilicate (TMOS) was hydrolyzed and polymerized under strongly acidic conditions in the presence of substoichiometric quantities of water. The polymerization reaction was monitored during 64 h using 29Si NMR and UV-Raman spectroscopy. The nature of the oligomers and the condensation reaction pathways were unraveled using this combination of experimental techniques together with molecular modeling. 29Si NMR and UV-Raman signals which previously were not documented in literature could be assigned. TMOS rapidly was converted into short straight methoxylated silicate chains. Subsequently the growth of oligomers proceeded by condensations between a hydrolyzed middle group of a chain with an end-group of another chain. Larger oligomers were attached to each other via condensations between middle groups generating multiply branched structures. Rings were formed late in the reaction scheme through internal condensations of sizable silicate molecules. Oligomers that were characteristic of the different stages of the polymerization process were proposed. Oligomerization pathways starting from tetramethylorthosilicate and tetraethylorthosilicate (TEOS) are significantly different. While with TMOS rings are formed only late in the oligomerization scheme, with TEOS rings are formed at early stages through cyclo-dimerization. This insight into the different nature of the oligomers obtained from TMOS and TEOS will assist the design of new silica sol–gel materials.

DOI

http://dx.doi.org/10.1021/jp109901v

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11 j. phys. chem. C 115, 11077 depla.pdf

ESA Prodex

wim — Tue, 23 Apr 2013 12:58:00 +0000

Project promotor

V. Van Speybroeck, M. Waroquier

Financierende instantie

ESA-PRODEX

Project data

01/01/2012 to 31/12/2013

Bedrag

€58 800,00

Project titel

Ordered Liquid Phases

Personeel

M. Van Houteghem

Project ref.

ESA

ESA Prodex

wim — Tue, 23 Apr 2013 12:53:51 +0000

Project promotor

V. Van Speybroeck, M. Waroquier

Financierende instantie

ESA-PRODEX

Project data

01/01/2009 to 31/12/2010

Bedrag

€55 000,00

Project titel

Ordered Liquid Phases

Personeel

M. Van Houteghem

Project ref.

ESA

Design of zeolite by inverse sigma transformation

michel — Mon, 03 Sep 2012 10:08:14 +0000

E. Verheyen, L. Joos, K. Van Havenbergh, N. Kasian, E. Gobechiya, K. Houthoofd, M. Hinterstein, E. Breynaerts, V. Van Speybroeck, M. Waroquier, S. Bals, G. Van Tendeloo, C. Kirschhock, J.A. Martens

Nature Materials

11 (12), 1059-1064

2012

Abstract

Zeolites are silicon materials, that have channels and pores on the nanoscale. This paper reports the synthesis of a new zeolite, in which the pores were widened using a revolutionary synthesis method. The final material has a series of unique and special properties, useful for industrial processes. Molecular modeling was used to determine the structure of the material.

Zeolieten zijn materialen opgebouwd uit silicium, die op nanoschaal kanalen en poriën bevatten. Deze paper rapporteert de synthese van een nieuw type zeoliet, waarbij de kanalen op een revolutionaire manier werden vergroot. Het eindmateriaal heeft daarom een hele reeks aan unieke en bijzonder interessante eigenschappen voor een aantal industriële processen. Moleculaire modelering werd gebruikt om de structuur van het materiaal te bepalen.

A graphical representation of COK14: