Center for Molecular Modeling - T. De Meyer

Acidity constant (pKa) calculation of large solvated dye molecules: evaluation of two advanced molecular dynamics methods

michel — Sat, 09 Jul 2016 19:46:50 +0000

T. De Meyer, B. Ensing, S.M.J. Rogge, K. De Clerck, E.J. Meijer, V. Van Speybroeck

ChemPhysChem

17 (21), 3447–3459

2016

Abstract

pH-sensitive dyes are increasingly applied onto polymer substrates for the creation of novel sensor materials. Recently, these dye molecules have been modified to form a covalent bond with the polymer host. This can have a large influence on the pH-sensitive properties, in particular on the acidity constant (pKa). Obtaining molecular control over the factors that influence the pK$_a$ value is mandatory for future intelligent design of sensor materials. Herein, we show that advanced molecular dynamics (MD) methods have reached the level where pKa values of large solvated dye molecules can be predicted with high accuracy. Two MD methods are used in this work: steered or restrained MD and the insertion/deletion scheme. Both are first calibrated on a set of phenol derivatives and afterwards applied to the dye molecule Bromothymol Blue. Excellent agreement with experimental values is obtained, which opens perspectives for using these methods for designing dye molecules.

Open Access version available at UGent repository

DOI

http://dx.doi.org/10.1002/cphc.201600734

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Meyer_et_al-2016-ChemPhysChem.pdf

Halochromic properties of sulfonphthaleine dyes in a textile environment: the influence of substituents

michel — Fri, 21 Aug 2015 19:52:13 +0000

T. De Meyer, I. Steyaert, K. Hemelsoet, R. Hoogenboom, V. Van Speybroeck, K. De Clerck

Dyes and Pigments

124 (2016), 249-257

2016

Abstract

The application of pH-sensitive dye molecules onto textile materials is a promising method for the development of sensor materials. Ten commonly used pH-indicators, namely sulfonphthaleine dyes, are applied onto polyamide 6 using two distinct methods: conventional dyeing of fabrics and dye-doping of nanofibres. The influence of the substituents of each dye on their interaction with polyamide, as well as the difference between both application methods is investigated. For the conventionally dyed fabrics, halogen substituents are needed to result in a pH-sensitive fabric. This can be traced back to halogen bonding and is supported by theoretical simulations. Dye-doped nanofibrous non-wovens show significant dye leaching, which can be understood based on the very acidic electrospinning solution. The use of a complexing agent improves the leaching properties, especially for dyes containing four bromine substituents. These findings indicate the importance of halogen substituents on sulfonphthaleines for further research in the development of pH-sensitive sensors.

Open Access version available at UGent repository

DOI

http://dx.doi.org/10.1016/j.dyepig.2015.09.007

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16-dyes-and-pigments-124(2016)249-demeyer.pdf

Exploring the Vibrational Fingerprint of the Electronic Excitation Energy via Molecular Dynamics

michel — Tue, 26 Nov 2013 20:29:14 +0000

A. Van Yperen-De Deyne, T. De Meyer, E. Pauwels, A. Ghysels, K. De Clerck, M. Waroquier, V. Van Speybroeck, K. Hemelsoet

Journal of Chemical Physics

140 (2014), 134105

2014

Abstract

A Fourier-based method is presented to relate changes of the molecular structure during a molecular dynamics simulation with fluctuations in the electronic excitation energy. The method implies sampling of the ground state potential energy surface. Subsequently, the power spectrum of the velocities is compared with the power spectrum of the excitation energy computed using time-dependent density functional theory. Peaks in both spectra are compared, and motions exhibiting a linear or quadratic behavior can be distinguished. The quadratically active motions are mainly responsible for the changes in the excitation energy and hence cause shifts between the dynamic and static values of the spectral property. Moreover, information about the potential energy surface of various excited states can be obtained. The procedure is illustrated with three case studies. The first electronic excitation is explored in detail and dominant vibrational motions responsible for changes in the excitation energy are identified for ethylene, biphenyl, and hexamethylbenzene. The proposed method is also extended to other low-energy excitations. Finally, the vibrational fingerprint of the excitation energy of a more complex molecule, in particular the azo dye ethyl orange in a water environment, is analyzed.

DOI

http://dx.doi.org/10.1063/1.4869937

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JChemPhys_140_134105 (Van Yperen-De Deyne et al., 2014).pdf

VanYperenDeDeyne2013-JCP-Revision-SI.pdf

Substituent effects on absorption spectra of pH-indicators: An experimental and computational study of sulfonphthaleine dyes

thierry — Wed, 02 Oct 2013 09:51:02 +0000

T. De Meyer, K. Hemelsoet, V. Van Speybroeck, K. De Clerck

Dyes and Pigments

102, 241-250

2014

Abstract

Sulfonphthaleine dyes are an important class of pH indicators, finding applications in novel (textile) sensors. In this paper, we present a combined experimental and theoretical study to elucidate the halochromic behaviour of a large set of sulfonphthaleine compounds. Starting from an experimental analysis consisting of UV/Vis spectroscopy, the pH region and the absorption wavelengths related to the colour shift are obtained and pKa values are derived. The effect of the substituents on the pH region can be traced back to their electron donating/withdrawing properties. Time-Dependent Density Functional Theory (TD-DFT) is able to adequately produce the trend in experimental wavelengths. Proton affinities are used to assess the effect of substituents on the pH region. The combination of theory and experiment is able to give a better understanding of the pH sensitivity; the methodology in this work will be useful in future dye design and is applicable to other dye classes as well.

Open Access version available at UGent repository

DOI

http://dx.doi.org/10.1016/j.dyepig.2013.10.048

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14_dyes&pigments_102(2014)241_DeMeyer.pdf

Identification of intermediates in zeolite-catalyzed reactions using in-situ UV/Vis micro-spectroscopy and a complementary set of molecular simulations

michel — Sat, 18 May 2013 20:05:23 +0000

K. Hemelsoet, Q. Qian, T. De Meyer, K. De Wispelaere, B. De Sterck, B.M. Weckhuysen, M. Waroquier, V. Van Speybroeck

Chemistry - A European Journal

19, 49, 16595-16606

2013

Abstract

The optical absorption properties of (poly)aromatic hydrocarbons occluded in a nanoporous environment were investigated by theoretical and experimental methods. The carbonaceous species are an essential part of a working catalyst for the methanol-to-olefins (MTO) process. In situ UV/Vis microscopy measurements on methanol conversion over the acidic solid catalysts H-SAPO-34 and H-SSZ-13 revealed the growth of various broad absorption bands around 400, 480, and 580 nm. The cationic nature of the involved species was determined by interaction of ammonia with the methanol-treated samples. To determine which organic species contribute to the various bands, a systematic series of aromatics was analyzed by means of time-dependent density functional theory (TDDFT) calculations. Static gas-phase simulations revealed the influence of structurally different hydrocarbons on the absorption spectra, whereas the influence of the zeolitic framework was examined by using supramolecular models within a quantum mechanics/molecular mechanics framework. To fully understand the origin of the main absorption peaks, a molecular dynamics (MD) study on the organic species trapped in the inorganic host was essential. During such simulation the flexibility is fully taken into account and the effect on the UV/Vis spectra is determined by performing TDDFT calculations on various snapshots of the MD run. This procedure allows an energy absorption scale to be provided and the various absorption bands determined from in situ UV/Vis spectra to be assigned to structurally different species.

DOI

http://dx.doi.org/10.1002/chem.201301965

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13_chem_eur_ j_xxx_Hemelsoet.pdf

Polycaprolactone and polycaprolactone/chitosan nanofibres functionalised with the pH-sensitive dye Nitrazine Yellow

hemel — Thu, 31 May 2012 12:04:11 +0000

L. Van der Schueren, T. De Meyer, I. Steyaert, O. Ceylan, K. Hemelsoet, V. Van Speybroeck, K. De Clerck

Carbohydrate Polymers

91 (1), 284-293

2013

Abstract

Nanofibres functionalised with pH-sensitive dyes could greatly contribute to the development of stimuli-responsive materials. However, the application of biocompatible polymers is vital to allow for their use in (bio)medical applications. Therefore, this paper focuses on the development and characterisation of pH-sensitive polycaprolactone (PCL) nanofibrous structures and PCL/chitosan nanofibrous blends with 20% chitosan. Electrospinning with added Nitrazine Yellow molecules proved to be an excellent method resulting in pH-responsive non-wovens. Unlike the slow and broad response of PCL nanofibres (time lag of more than 3 h), the use of blends with chitosan led to an increased sensitivity and significantly reduced response time (time lag of 5 min). These important effects are attributed to the increased hydrophilic nature of the nanofibres containing chitosan. Computational calculations indicated stronger interactions, mainly based on electrostatic interactions, of the dye with chitosan (ΔG of -132.3 kJ/mol) compared to the long-range interactions with PCL (ΔG of -35.6 kJ/mol), thus underpinning our experimental observations. In conclusion, because of the unique characteristics of chitosan, the use of PCL/chitosan blends in pH-sensitive biocompatible nanofibrous sensors is crucial.

Open Access version available at UGent repository

DOI

http://dx.doi.org/10.1016/j.carbpol.2012.08.003

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13 carbo. polymers 91(1)284 Van.derScheuren.pdf

Investigating the Halochromic Properties of Azo Dyes in an Aqueous Environment by Using a Combined Experimental and Theoretical Approach

michel — Wed, 23 Nov 2011 13:27:56 +0000

T. De Meyer, K. Hemelsoet, L. Van der Schueren, E. Pauwels, K. De Clerck, V. Van Speybroeck

Chemistry - A European Journal

18 (26), 8120-8129

2012

Abstract

The halochromism in solution of a prototypical example of an azo dye, ethyl orange, was investigated by using a combined theoretical and experimental approach. Experimental UV/Vis and Raman spectroscopy pointed towards a structural change of the azo dye with changing pH value (in the range pH 5–3). The pH-sensitive behavior was modeled through a series of ab initio computations on the neutral and various singly and doubly protonated structures. For this purpose, contemporary DFT functionals (B3LYP, CAM-B3LYP, and M06) were used in combination with implicit modeling of the water solvent environment. Static calculations were successful in assigning the most-probable protonation site. However, to fully understand the origin of the main absorption peaks, a molecular dynamics simulation study in a water molecular environment was used in combination with time-dependent DFT (TD-DFT) calculations to deduce average UV/Vis spectra that take into account the flexibility of the dye and the explicit interactions with the surrounding water molecules. This procedure allowed us to achieve a remarkable agreement between the theoretical and experimental UV/Vis spectrum and enabled us to fully unravel the pH-sensitive behavior of ethyl orange in aqueous environment.

DOI

http://dx.doi.org/10.1002/chem.201103633

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12_chem_eur_j_18(26)8120_DeMeyer.pdf

Experimental and computational study of the pH-sensitive properties of organic dye molecules

wim — Mon, 26 Sep 2016 10:43:18 +0000

T. De Meyer

Tue, 20/09/2016

Faculty of Engineering and Architecture, Jozef Plateaustraat, Ghent

http://hdl.handle.net/1854/LU-8088230

Supervisors

Prof. Dr. ir. Veronique Van Speybroeck, Prof. Dr. ir. Karen De Clerck

252nd ACS National Meeting & Exposition

wim — Thu, 30 Jun 2016 06:23:32 +0000

Philadelphia, USA

Sunday, 21 August, 2016 to Thursday, 25 August, 2016

Participant(s)

K. De Wispelaere, J. Hajek, T. De Meyer

Project ref.

ERC DYNPOR H20ERC2015000301

Conference reference

252nd ACS National Meeting & Exposition

TACC 2016

wim — Mon, 30 May 2016 11:17:41 +0000

Seattle, USA

Sunday, 28 August, 2016 to Friday, 2 September, 2016

Participant(s)

T. De Meyer

Project ref.

BOF T. De Meyer BOFDOC2014003501

Conference reference

TACC 2016