Acidity Constant (pKa ) Calculation of Large Solvated Dye Molecules: Evaluation of Two Advanced Molecular Dynamics Methods.

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

Exploring the vibrational fingerprint of the electronic excitation energy via molecular dynamics.

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.

Identification of intermediates in zeolite-catalyzed reactions by in situ UV/Vis microspectroscopy and a complementary set of molecular simulations.

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.

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

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 3h), 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.

Investigating the halochromic properties of azo dyes in an aqueous environment by using a combined experimental and theoretical approach.

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.