Center for Molecular Modeling - M. Van Houteghem

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

Private attachment

14_j_phys_chem_b_xxxx_VanHouteghem.pdf

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

Private attachment

12 J. Chem. Phys. 137 104506 VanHouteghem.pdf

12 J. Chem. Phys. draft VanHouteghem.pdf

MD-TRACKS: A Productive Solution for the Advanced Analysis of Molecular Dynamics and Monte Carlo simulations

wim — Mon, 03 Oct 2011 10:02:05 +0000

T. Verstraelen, M. Van Houteghem, V. Van Speybroeck, M. Waroquier

Journal of Chemical Information and Modeling (JCIM)

48 (12), 2414–2424

2008

Abstract

In this paper, we present MD-TRACKS, an advanced statistical analysis toolkit for Molecular Dynamics and Monte Carlo simulations. The program is compatible with different molecular simulation codes, and the analysis results can be loaded into spreadsheet software and plotting tools. The analysis is performed with commands that operate on a binary trajectory database. These commands process not only plain trajectory data but also the output of other MD-TRACKS commands, which enables complex analysis work flows that are easily programmed in shell scripts. The applicability, capabilities, and ease of use of MD-TRACKS are illustrated by means of examples, that is, the construction of vibrational spectra and radial distribution functions from a molecular dynamics run is discussed in the case of tetrahydrofuran. These properties are compared with the experimental data available in the literature. MD-TRACKS is open-source software distributed at http://molmod.ugent.be/code/.

DOI

http://dx.doi.org/10.1021/ci800233y

Private attachment

08 j. chem. inf. model 48(12)2414 verstraelen.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

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

Private attachment

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

Critical analysis of liquid structure models

wim — Wed, 15 Oct 2014 06:36:49 +0000

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

ISBN/ISSN:

Invited talk

Conference / event / venue

WATOC 2014

Santiago de Chile, Chile

Sunday, 5 October, 2014 to Friday, 10 October, 2014

Abstract (private)

2014_WATOC_liquidstructure.pdf

Conference reference

WATOC 2014

Molecular dynamics simulations as a tool for understanding zeolite nanogrowth and liquid structure

wim — Fri, 18 Oct 2013 11:51:08 +0000

M. Van Houteghem

Mon, 16/12/2013

Faculty of Engineering and Architecture, Jozef Plateaustraat, Ghent

http://hdl.handle.net/1854/LU-4228273

Supervisors

Prof. Dr. ir. Veronique Van Speybroeck, Prof. Dr. Michel Waroquier

Attachment (private)

phd_MarcVanHouteghem_okt.pdf

SBO POXPEG

wim — Wed, 15 May 2013 13:34:50 +0000

Project promotor

V. Van Speybroeck

Financierende instantie

SBO-IWT

Project data

01/02/2013 to 31/01/2015

Bedrag

€120 000,00

Project titel

POXilation asnext generation PEGylation

Personeel

D. Hertsen, M. Van Houteghem, H. Goossens

Extra info

Andere partners: R. Hoogenboom / R. Beyaert

Project ref.

SBO POXPEG B/13515/*

BOF-GOA (BOF06)

wim — Thu, 25 Apr 2013 09:49:30 +0000

Project promotor

N. De Kimpe, M. Waroquier, V. Van Speybroeck

Financierende instantie

BOF-GOA

Project data

01/01/2007 to 31/08/2013

Bedrag

€700 000,00

Project titel

Exploration of fundamental reactions on heterocyclic compounds guided by ab initio molecular modeling.

Personeel

B. De Sterck, P. Vansteenkiste, D.D. Claeys, M. Van Houteghem, S. Catak, D. Hertsen, S.L. Moors, A. Van Yperen-De Deyne

Extra info

Bedrag: partim CMM

Project ref.

GOA06

IAP VI

wim — Tue, 23 Apr 2013 13:49:35 +0000

Project promotor

M. Waroquier, V. Van Speybroeck

Financierende instantie

BELSPO

Project data

01/01/2007 to 31/12/2011

Bedrag

€550 000,00

Project titel

Functional Supramolecular Systems (FS2)

Personeel

T. Verstraelen, W. Dewitte, M. Van Houteghem, S. Cottenier, M. Vandichel, S. Catak

Project ref.

IAP VI P6/27